Isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficiency

ABSTRACT

Provided are isolated polynucleotides encoding a polypeptide at least 80% homologous to the amino acid sequence selected from the group consisting of SEQ ID NOs: 757, 456-756, 758-774, 8385-10836, and 10838-14462; and isolated polynucleotide comprising nucleic acid sequences at least 80% identical to SEQ ID NO: 377, 1-376, 378-455, and 775-8384. Also provided are nucleic acid constructs comprising same, isolated polypeptides encoded thereby, transgenic cells and transgenic plants comprising same and methods of using same for increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant.

RELATED APPLICATIONS

This application is a division of U.S. patent application Ser. No.16/234,643 filed on Dec. 28, 2018, which is a continuation of U.S.patent application Ser. No. 14/115,397 filed on Nov. 4, 2013, now U.S.Pat. No. 10,760,088, which is a National Phase of PCT Patent ApplicationNo. PCT/IL2012/050154 having International Filing Date of May 2, 2012,which claims the benefit of priority under 35 USC § 119(e) of U.S.Provisional Patent Application No. 61/481,752 filed on May 3, 2011 and61/537,621 filed on Sep. 22, 2011.

The contents of the above applications are all incorporated by referenceas if fully set forth herein in their entirety.

SEQUENCE LISTING STATEMENT

The ASCII file, entitled 88066SequenceListing.txt, created on Jul. 15,2021, comprising 33,138,135 bytes, submitted concurrently with thefiling of this application is incorporated herein by reference.

FIELD AND BACKGROUND OF THE INVENTION

The present invention, in some embodiments thereof, relates to isolatedpolypeptides and polynucleotides, nucleic acid constructs comprisingsame, transgenic cells comprising same, transgenic plants exogenouslyexpressing same and more particularly, but not exclusively, to methodsof using same for increasing yield (e.g., seed yield, oil yield),biomass, growth rate, vigor, oil content, fiber yield, fiber qualityabiotic stress tolerance, and/or fertilizer use efficiency (e.g.,nitrogen use efficiency) of a plant.

A common approach to promote plant growth has been, and continues to be,the use of natural as well as synthetic nutrients (fertilizers). Thus,fertilizers are the fuel behind the “green revolution”, directlyresponsible for the exceptional increase in crop yields during the last40 years, and are considered the number one overhead expense inagriculture. Of the three macronutrients provided as main fertilizers[Nitrogen (N), Phosphate (P) and Potassium (K)], nitrogen is often therate-limiting element in plant growth and all field crops have afundamental dependence on inorganic nitrogenous fertilizer. Nitrogenusually needs to be replenished every year, particularly for cereals,which comprise more than half of the cultivated areas worldwide. Forexample, inorganic nitrogenous fertilizers such as ammonium nitrate,potassium nitrate, or urea, typically accounts for 40% of the costsassociated with crops such as corn and wheat.

Nitrogen is an essential macronutrient for the plant, responsible forbiosynthesis of amino and nucleic acids, prosthetic groups, planthormones, plant chemical defenses, etc. In addition, nitrogen is oftenthe rate-limiting element in plant growth and all field crops have afundamental dependence on inorganic nitrogen. Thus, nitrogen istranslocated to the shoot, where it is stored in the leaves and stalkduring the rapid step of plant development and up until flowering. Incorn for example, plants accumulate the bulk of their organic nitrogenduring the period of grain germination, and until flowering. Oncefertilization of the plant has occurred, grains begin to form and becomethe main sink of plant nitrogen. The stored nitrogen can be thenredistributed from the leaves and stalk that served as storagecompartments until grain formation.

Since fertilizer is rapidly depleted from most soil types, it must besupplied to growing crops two or three times during the growing season.In addition, the low nitrogen use efficiency (NUE) of the main crops(e.g., in the range of only 30-70%) negatively affects the inputexpenses for the farmer, due to the excess fertilizer applied. Moreover,the over and inefficient use of fertilizers are major factorsresponsible for environmental problems such as eutrophication ofgroundwater, lakes, rivers and seas, nitrate pollution in drinking waterwhich can cause methemoglobinemia, phosphate pollution, atmosphericpollution and the like. However, in spite of the negative impact offertilizers on the environment, and the limits on fertilizer use, whichhave been legislated in several countries, the use of fertilizers isexpected to increase in order to support food and fiber production forrapid population growth on limited land resources.

For example, it has been estimated that by 2050, more than 150 milliontons of nitrogenous fertilizer will be used worldwide annually.

Increased use efficiency of nitrogen by plants should enable crops to becultivated with lower fertilizer input, or alternatively to becultivated on soils of poorer quality and would therefore havesignificant economic impact in both developed and developingagricultural systems.

Genetic improvement of fertilizer use efficiency (FUE) in plants can begenerated either via traditional breeding or via genetic engineering.

Attempts to generate plants with increased FUE have been described inU.S. Pat. Appl. No. 20020046419 to Choo, et al.; U.S. Pat. Appl. No.20050108791 to Edgerton et al.; U.S. Pat. Appl. No. 20060179511 toChomet et al.; Good, A, et al. 2007 (Engineering nitrogen use efficiencywith alanine aminotransferase. Canadian Journal of Botany 85: 252-262);and Good A G et al. 2004 (Trends Plant Sci. 9:597-605).

Yanagisawa et al. (Proc. Natl. Acad. Sci. U.S.A. 2004 101:7833-8)describe Dof1 transgenic plants which exhibit improved growth underlow-nitrogen conditions.

U.S. Pat. No. 6,084,153 to Good et al. discloses the use of a stressresponsive promoter to control the expression of Alanine AmineTransferase (AlaAT) and transgenic canola plants with improved droughtand nitrogen deficiency tolerance when compared to control plants.

The ever-increasing world population and the decreasing availability inarable land for agriculture affect the yield of plants and plant-relatedproducts. The global shortage of water supply, desertification, abioticstress (ABS) conditions (e.g., salinity, drought, flood, suboptimaltemperature and toxic chemical pollution), and/or limited nitrogen andfertilizer sources cause substantial damage to agricultural plants suchas major alterations in the plant metabolism, cell death, and decreasesin plant growth and crop productivity.

Drought is a gradual phenomenon, which involves periods of abnormallydry weather that persists long enough to produce serious hydrologicimbalances such as crop damage, water supply shortage and increasedsusceptibility to various diseases.

Salinity, high salt levels, affects one in five hectares of irrigatedland. None of the top five food crops, i.e., wheat, corn, rice,potatoes, and soybean, can tolerate excessive salt. Detrimental effectsof salt on plants result from both water deficit, which leads to osmoticstress (similar to drought stress), and the effect of excess sodium ionson critical biochemical processes. As with freezing and drought, highsalt causes water deficit; and the presence of high salt makes itdifficult for plant roots to extract water from their environment. Thus,salination of soils that are used for agricultural production is asignificant and increasing problem in regions that rely heavily onagriculture, and is worsen by over-utilization, over-fertilization andwater shortage, typically caused by climatic change and the demands ofincreasing population.

Suboptimal temperatures affect plant growth and development through thewhole plant life cycle. Thus, low temperatures reduce germination rateand high temperatures result in leaf necrosis. In addition, matureplants that are exposed to excess of heat may experience heat shock,which may arise in various organs, including leaves and particularlyfruit, when transpiration is insufficient to overcome heat stress. Heatalso damages cellular structures, including organelles and cytoskeleton,and impairs membrane function. Heat shock may produce a decrease inoverall protein synthesis, accompanied by expression of heat shockproteins, e.g., chaperones, which are involved in refolding proteinsdenatured by heat. High-temperature damage to pollen almost alwaysoccurs in conjunction with drought stress, and rarely occurs underwell-watered conditions. Combined stress can alter plant metabolism innovel ways. Excessive chilling conditions, e.g., low, but abovefreezing, temperatures affect crops of tropical origins, such assoybean, rice, maize, and cotton. Typical chilling damage includeswilting, necrosis, chlorosis or leakage of ions from cell membranes.Excessive light conditions, which occur under clear atmosphericconditions subsequent to cold late summer/autumn nights, can lead tophotoinhibition of photosynthesis (disruption of photosynthesis). Inaddition, chilling may lead to yield losses and lower product qualitythrough the delayed ripening of maize.

Nutrient deficiencies cause adaptations of the root architecture,particularly notably for example is the root proliferation withinnutrient rich patches to increase nutrient uptake. Nutrient deficienciescause also the activation of plant metabolic pathways which maximize theabsorption, assimilation and distribution processes such as byactivating architectural changes. Engineering the expression of thetriggered genes may cause the plant to exhibit the architectural changesand enhanced metabolism also under other conditions.

In addition, it is widely known that the plants usually respond to waterdeficiency by creating a deeper root system that allows access tomoisture located in deeper soil layers. Triggering this effect willallow the plants to access nutrients and water located in deeper soilhorizons particularly those readily dissolved in water like nitrates.

Yield is affected by various factors, such as, the number and size ofthe plant organs, plant architecture (for example, the number ofbranches), grains set length, number of filled grains, vigor (e.g.seedling), growth rate, root development, utilization of water,nutrients (e.g., nitrogen) and fertilizers, and stress tolerance.

Crops such as, corn, rice, wheat, canola and soybean account for overhalf of total human caloric intake, whether through direct consumptionof the seeds themselves or through consumption of meat products raisedon processed seeds or forage. Seeds are also a source of sugars,proteins and oils and metabolites used in industrial processes. Theability to increase plant yield, whether through increase dry matteraccumulation rate, modifying cellulose or lignin composition, increasestalk strength, enlarge meristem size, change of plant branchingpattern, erectness of leaves, increase in fertilization efficiency,enhanced seed dry matter accumulation rate, modification of seeddevelopment, enhanced seed filling or by increasing the content of oil,starch or protein in the seeds would have many applications inagricultural and non-agricultural uses such as in the biotechnologicalproduction of pharmaceuticals, antibodies or vaccines.

Studies have shown that plant adaptations to adverse environmentalconditions are complex genetic traits with polygenic nature.Conventional means for crop and horticultural improvements utilizeselective breeding techniques to identify plants having desirablecharacteristics. However, selective breeding is tedious, time consumingand has an unpredictable outcome. Furthermore, limited germplasmresources for yield improvement and incompatibility in crosses betweendistantly related plant species represent significant problemsencountered in conventional breeding. Advances in genetic engineeringhave allowed mankind to modify the germplasm of plants by expression ofgenes-of-interest in plants. Such a technology has the capacity togenerate crops or plants with improved economic, agronomic orhorticultural traits.

WO publication No. 2009/013750 discloses genes, constructs and methodsof increasing abiotic stress tolerance, biomass and/or yield in plantsgenerated thereby.

WO publication No. 2008/122980 discloses genes constructs and methodsfor increasing oil content, growth rate and biomass of plants.

WO publication No. 2008/075364 discloses polynucleotides involved inplant fiber development and methods of using same.

WO publication No. 2007/049275 discloses isolated polypeptides,polynucleotides encoding same, transgenic plants expressing same andmethods of using same for increasing fertilizer use efficiency, plantabiotic stress tolerance and biomass.

WO publication No. 2004/104162 discloses methods of increasing abioticstress tolerance and/or biomass in plants and plants generated thereby.

WO publication No. 2005/121364 discloses polynucleotides andpolypeptides involved in plant fiber development and methods of usingsame for improving fiber quality, yield and/or biomass of a fiberproducing plant.

WO publication No. 2007/020638 discloses methods of increasing abioticstress tolerance and/or biomass in plants and plants generated thereby.

WO publication No. 2009/083958 discloses methods of increasing water useefficiency, fertilizer use efficiency, biotic/abiotic stress tolerance,yield and biomass in plant and plants generated thereby.

WO publication No. 2010/020941 discloses methods of increasing nitrogenuse efficiency, abiotic stress tolerance, yield and biomass in plantsand plants generated thereby.

WO publication No. 2009/141824 discloses isolated polynucleotides andmethods using same for increasing plant utility.

WO publication No. 2010/076756 discloses isolated polynucleotides forincreasing abiotic stress tolerance, yield, biomass, growth rate, vigor,oil content, fiber yield, fiber quality, and/or nitrogen use efficiencyof a plant.

WO publication No. 2004/081173 discloses novel plant derived regulatorysequences and constructs and methods of using such sequences fordirecting expression of exogenous polynucleotide sequences in plants.

WO publication No. 2010/049897 discloses isolated polynucleotides andpolypeptides and methods of using same for increasing plant yield,biomass, growth rate, vigor, oil content, abiotic stress tolerance ofplants and nitrogen use efficiency.

WO publication No. 2004/111183 discloses nucleotide sequences forregulating gene expression in plant trichomes and constructs and methodsutilizing same.

WO publication No. 2011/080674 discloses isolated polynucleotides andpolypeptides and methods of using same for increasing plant yield,biomass, growth rate, vigor, oil content, abiotic stress tolerance ofplants and nitrogen use efficiency.

WO2010/100595 publication discloses isolated polynucleotides andpolypeptides, and methods of using same for increasing plant yieldand/or agricultural characteristics.

WO2011/015985 publication discloses polynucleotides and polypeptides forincreasing desirable plant qualities.

WO2010/143138 publication discloses isolated polynucleotides andpolypeptides, and methods of using same for increasing nitrogen useefficiency, fertilizer use efficiency, yield, growth rate, vigor,biomass, oil content, abiotic stress tolerance and/or water useefficiency.

SUMMARY OF THE INVENTION

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing yield, biomass, growth rate,vigor, oil content, fiber yield, fiber quality, abiotic stresstolerance, and/or nitrogen use efficiency of a plant, comprisingexpressing within the plant an exogenous polynucleotide comprising anucleic acid sequence encoding a polypeptide at least 80% identical toSEQ ID NO: 456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575,12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615,12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677,12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717,12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825,12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886,12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926,12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967,12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003,13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049,13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076,13079-13084, 13086-14461 or 14462, thereby increasing the yield,biomass, growth rate, vigor, oil content, fiber yield, fiber quality,abiotic stress tolerance, and/or nitrogen use efficiency of the plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing yield, biomass, growth rate,vigor, oil content, fiber yield, fiber quality, abiotic stresstolerance, and/or nitrogen use efficiency of a plant, comprisingexpressing within the plant an exogenous polynucleotide comprising anucleic acid sequence encoding a polypeptide selected from the groupconsisting of SEQ ID NOs:456-774, 8385-10836, 10838-14461 and 14462,thereby increasing the yield, biomass, growth rate, vigor, oil content,fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogenuse efficiency of the plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing yield, biomass, growth rate,vigor, oil content, fiber yield, fiber quality, abiotic stresstolerance, and/or nitrogen use efficiency of a plant, comprisingexpressing within the plant an exogenous polynucleotide comprising anucleic acid sequence at least 80% identical to SEQ ID NO: 1-455,775-6485, 6487-6657, 6660-6664, 6666-6701, 6703-6745, 6748-6818,6820-6821, 6824-6827, 6829-6881, 6883, 6885-8383 or 8384, therebyincreasing the yield, biomass, growth rate, vigor, oil content, fiberyield, fiber quality, abiotic stress tolerance, and/or nitrogen useefficiency of the plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing yield, biomass, growth rate,vigor, oil content, fiber yield, fiber quality, abiotic stresstolerance, and/or nitrogen use efficiency of a plant, comprisingexpressing within the plant an exogenous polynucleotide comprising thenucleic acid sequence selected from the group consisting of SEQ ID NOs:1-455, 775-8383 and 8384, thereby increasing the yield, biomass, growthrate, vigor, oil content, fiber yield, fiber quality, abiotic stresstolerance, and/or nitrogen use efficiency of the plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing nitrogen use efficiency and/oroil content of a plant, comprising expressing within the plant anexogenous polynucleotide comprising a nucleic acid sequence encoding apolypeptide at least 80% identical to SEQ ID NO: 10837, therebyincreasing the nitrogen use efficiency and/or oil content of the plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing nitrogen use efficiency and/oroil content of a plant, comprising expressing within the plant anexogenous polynucleotide comprising a nucleic acid sequence encoding thepolypeptide set forth in SEQ ID NO:10837, thereby increasing thenitrogen use efficiency and/or oil content of the plant.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polynucleotide comprising a nucleic acidsequence encoding a polypeptide which comprises an amino acid sequenceat least 80% homologous to the amino acid sequence set forth in SEQ IDNO: 456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577,12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624,12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681,12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727,12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840,12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887,12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937,12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977,12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010,13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054,13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084,13086-14461 or 14462, wherein the amino acid sequence is capable ofincreasing yield, biomass, growth rate, vigor, oil content, fiber yield,fiber quality, abiotic stress tolerance, and/or nitrogen use efficiencyof a plant.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polynucleotide comprising a nucleic acidsequence encoding a polypeptide which comprises the amino acid sequenceselected from the group consisting of SEQ ID NOs:456-774, 8385-10836,10838-14461 and 14462.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polynucleotide comprising a nucleic acidsequence at least 80% identical to SEQ ID NO:1-455, 775-6485, 6487-6657,6660-6664, 6666-6701, 6703-6745, 6748-6818, 6820-6821, 6824-6827,6829-6881, 6883, 6885-8383, or 8384, wherein the nucleic acid sequenceis capable of increasing yield, biomass, growth rate, vigor, oilcontent, fiber yield, fiber quality, abiotic stress tolerance, and/ornitrogen use efficiency of a plant.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polynucleotide comprising the nucleic acidsequence selected from the group consisting of SEQ ID NOs: 1-455,775-8383 and 8384.

According to an aspect of some embodiments of the present inventionthere is provided a nucleic acid construct comprising the isolatedpolynucleotide of some embodiments of the invention, and a promoter fordirecting transcription of the nucleic acid sequence in a host cell.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polypeptide comprising an amino acidsequence at least 80% homologous to SEQ ID NO: 456-774, 8385-8643,8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586,12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659,12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705,12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813,12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853,12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896,12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942,12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984,12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016,13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063,13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 or14462, wherein the amino acid sequence is capable of increasing yield,biomass, growth rate, vigor, oil content, fiber yield, fiber quality,abiotic stress tolerance, and/or nitrogen use efficiency of a plant.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polypeptide comprising the amino acidsequence selected from the group consisting of SEQ ID NOs: 456-774,8385-10836, and 10838-14462.

According to an aspect of some embodiments of the present inventionthere is provided a plant cell exogenously expressing the polynucleotideof some embodiments of the invention, or the nucleic acid construct ofsome embodiments of the invention.

According to an aspect of some embodiments of the present inventionthere is provided a plant cell exogenously expressing the polypeptide ofsome embodiments of the invention.

According to an aspect of some embodiments of the present inventionthere is provided a transgenic plant comprising the nucleic acidconstruct of some embodiments of the invention.

According to an aspect of some embodiments of the present inventionthere is provided a method of generating a transgenic plant, comprisingexpressing the nucleic acid construct of some embodiments of theinvention within the plant, thereby generating the transgenic plant.

According to some embodiments of the invention, the nucleic acidsequence encodes an amino acid sequence selected from the groupconsisting of SEQ ID NOs: 456-774, 8385-10836, and 10838-14462.

According to some embodiments of the invention, the nucleic acidsequence is selected from the group consisting of SEQ ID NOs: 1-455, and775-8384.

According to some embodiments of the invention, the polynucleotideconsists of the nucleic acid sequence selected from the group consistingof SEQ ID NOs: 1-455, and 775-8384.

According to some embodiments of the invention, the nucleic acidsequence encodes the amino acid sequence selected from the groupconsisting of SEQ ID NOs:456-774, 8385-10836, and 10838-14462.

According to some embodiments of the invention, the plant cell formspart of a plant.

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder the abiotic stress condition(s).

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder the nitrogen-limiting condition(s).

According to some embodiments of the invention, the abiotic stress isselected from the group consisting of salinity, drought, waterdeprivation, flood, etiolation, low temperature, high temperature, heavymetal toxicity, anaerobiosis, nutrient deficiency, nutrient excess,atmospheric pollution and UV irradiation.

According to some embodiments of the invention, the yield comprises seedyield or oil yield.

According to some embodiments of the invention, the promoter isheterologous the isolated polynucleotide and/or to the host cell.

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder nitrogen-limiting conditions.

Unless otherwise defined, all technical and/or scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which the invention pertains. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of embodiments of the invention, exemplarymethods and/or materials are described below. In case of conflict, thepatent specification, including definitions, will control. In addition,the materials, methods, and examples are illustrative only and are notintended to be necessarily limiting.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

Some embodiments of the invention are herein described, by way ofexample only, with reference to the accompanying drawings. With specificreference now to the drawings in detail, it is stressed that theparticulars shown are by way of example and for purposes of illustrativediscussion of embodiments of the invention. In this regard, thedescription taken with the drawings makes apparent to those skilled inthe art how embodiments of the invention may be practiced.

In the drawings:

FIG. 1 is a schematic illustration of the modified pGI binary plasmidcontaining the new At6669 promoter (SEQ ID NO: 14467) and the GUSintron(pQYN 6669) used for expressing the isolated polynucleotide sequences ofthe invention. RB—T-DNA right border; LB—T-DNA left border; MCS—Multiplecloning site; RE—any restriction enzyme; NOS pro=nopaline synthasepromoter; NPT-II=neomycin phosphotransferase gene; NOS ter=nopalinesynthase terminator, Poly-A signal (polyadenylation signal);GUSintron—the GUS reporter gene (coding sequence and intron). Theisolated polynucleotide sequences of the invention were cloned into thevector while replacing the GUSintron reporter gene.

FIG. 2 is a schematic illustration of the modified pGI binary plasmidcontaining the new At6669 promoter (SEQ ID NO: 14467) (pQFN or pQFNc)used for expressing the isolated polynucleotide sequences of theinvention. RB—T-DNA right border; LB—T-DNA left border; MCS—Multiplecloning site; RE—any restriction enzyme; NOS pro=nopaline synthasepromoter, NPT-II=neomycin phosphotransferase gene; NOS ter=nopalinesynthase terminator, Poly-A signal (polyadenylation signal); Theisolated polynucleotide sequences of the invention were cloned into theMCS of the vector.

FIGS. 3A-3F are images depicting visualization of root development oftransgenic plants exogenously expressing the polynucleotide of someembodiments of the invention when grown in transparent agar plates undernormal (FIGS. 3A-3B), osmotic stress (15% PEG; FIGS. 3C-3D) ornitrogen-limiting (FIGS. 3E-3F) conditions. The different transgeneswere grown in transparent agar plates for 17 days (7 days nursery and 10days after transplanting). The plates were photographed every 3-4 daysstarting at day 1 after transplanting. FIG. 3A—An image of a photographof plants taken following 10 after transplanting days on agar plateswhen grown under normal (standard) conditions. FIG. 3B—An image of rootanalysis of the plants shown in FIG. 3A in which the lengths of theroots measured are represented by arrows. FIG. 3C—An image of aphotograph of plants taken following 10 days after transplanting on agarplates, grown under high osmotic (PEG 15%) conditions. FIG. 3D—An imageof root analysis of the plants shown in FIG. 3C in which the lengths ofthe roots measured are represented by arrows. FIG. 3E—An image of aphotograph of plants taken following 10 days after transplanting on agarplates, grown under low nitrogen conditions. FIG. 3F—An image of rootanalysis of the plants shown in FIG. 3E in which the lengths of theroots measured are represented by arrows.

FIG. 4 is a schematic illustration of the modified pGI binary plasmidcontaining the Root Promoter (pQNa RP) used for expressing the isolatedpolynucleotide sequences of the invention. RB-T-DNA right border,LB—T-DNA left border; NOS pro=nopaline synthase promoter,NPT-II=neomycin phosphotransferase gene; NOS ter=nopaline synthaseterminator; Poly-A signal (polyadenylation signal); The isolatedpolynucleotide sequences according to some embodiments of the inventionwere cloned into the MCS (Multiple cloning site) of the vector.

FIG. 5 is a schematic illustration of the pQYN plasmid.

FIG. 6 is a schematic illustration of the pQFN plasmid.

FIG. 7 is a schematic illustration of the pQFYN plasmid.

FIG. 8 is a schematic illustration of the modified pGI binary plasmid(pQXNc) used for expressing the isolated polynucleotide sequences ofsome embodiments of the invention. RB—T-DNA right border; LB—T-DNA leftborder; NOS pro=nopaline synthase promoter; NPT-II=neomycinphosphotransferase gene; NOS ter=nopaline synthase terminator; RE=anyrestriction enzyme; Poly-A signal (polyadenylation signal); 35S—the 35Spromoter (SEQ ID NO: 14463). The isolated polynucleotide sequences ofsome embodiments of the invention were cloned into the MCS (Multiplecloning site) of the vector.

DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION

The present invention, in some embodiments thereof, relates to isolatedpolynucleotides and polypeptides, nucleic acid constructs encoding same,cells expressing same, transgenic plants expressing same and methods ofusing same for increasing yield, biomass, growth rate, vigor, oilcontent, fiber yield, fiber quality, abiotic stress tolerance, and/ornitrogen use efficiency of a plant.

Before explaining at least one embodiment of the invention in detail, itis to be understood that the invention is not necessarily limited in itsapplication to the details set forth in the following description orexemplified by the Examples. The invention is capable of otherembodiments or of being practiced or carried out in various ways.

The present inventors have identified novel polypeptides andpolynucleotides which can be used to increase yield, biomass, growthrate, vigor, oil content, fiber yield, fiber quality abiotic stresstolerance, and/or fertilizer use efficiency (e.g., nitrogen useefficiency) of a plant.

Thus, as shown in the Examples section which follows, the presentinventors have utilized bioinformatics tools to identify polynucleotideswhich enhance yield (e.g., seed yield, oil yield, oil content), growthrate, biomass, vigor, fiber yield, fiber quality, abiotic stresstolerance and/or nitrogen use efficiency) of a plant. Genes which affectthe trait-of-interest were identified [Table 53, Example 12, SEQ ID NOs:1-455 (polynucleotides) and SEQ ID NOs: 456-774 (polypeptides)] based oncorrelation analyses performed using Arabidopsis ecotypes (Examples 2and 3), tomato varieties (Example 4), B. juncea ecotypes (Examples 5 and6), Sorghum varieties (Example 7), Maize hybrids (Example 8), Soybeanvarieties (Example 9), Barley accessions (Example 10) and Cotton species(Examples 11) and the expression profiles of the genes according toselected expression sets (e.g., tissues, developmental stages and stressconditions) (Tables 1-53, Examples 1-12). Homologous polypeptides andpolynucleotides having the same function were also identified [Table 54,Example 13; SEQ ID NOs: 775-8384 (polynucleotides) and SEQ ID NOs:8385-14462 (polypeptides)]. The identified polynucleotides were clonedinto binary vectors (Example 14) and transgenic plants over-expressingthe identified polynucleotides and polypeptides were generated (Example15) and further evaluated for the effect of the exogenous gene on thetrait of interest (e.g., increased fresh and dry weight, leaf area, rootcoverage and length, relative growth rate (RGR) of leaf area, RGR ofroot coverage, RGR of root length, seed yield, oil yield, dry matter,harvest index, growth rate, rosette area, rosette diameter, RGR leafnumber, RGR plot coverage, RGR rosette diameter, leaf blade area, oilpercentage in seed and weight of 1000 seeds, plot coverage, tolerance toabiotic stress conditions and to fertilizer limiting conditions;Examples 16-18). Altogether, these results suggest the use of the novelpolynucleotides and polypeptides of the invention for increasing yield(including oil yield, seed yield and oil content), growth rate, biomass,vigor, fiber yield, fiber quality, abiotic stress tolerance and/ornitrogen use efficiency of a plant.

Thus, according to an aspect of some embodiments of the invention, thereis provided method of increasing yield, growth rate, biomass, vigor, oilcontent, fiber yield, fiber quality, fertilizer use efficiency (e.g.,nitrogen use efficiency) and/or abiotic stress tolerance of a plant,comprising expressing within the plant an exogenous polynucleotidecomprising a nucleic acid sequence encoding a polypeptide at least about80%, at least about 81%, at least about 82%, at least about 83%, atleast about 84%, at least about 85%, at least about 86%, at least about87%, at least about 88%, at least about 89%, at least about 90%, atleast about 91%, at least about 92%, at least about 93%, at least about94%, at least about 95%, at least about 96%, at least about 97%, atleast about 98%, at least about 99%, or more say 100% homologous to theamino acid sequence selected from the group consisting of SEQ ID NOs:456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577,12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624,12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681,12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727,12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840,12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887,12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937,12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977,12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010,13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054,13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084,13086-14461 and 14462, thereby increasing the yield, growth rate,biomass, vigor, oil content, fiber yield, fiber quality, fertilizer useefficiency (e.g., nitrogen use efficiency) and/or abiotic stresstolerance of the plant.

As used herein the phrase “plant yield” refers to the amount (e.g., asdetermined by weight or size) or quantity (numbers) of tissues or organsproduced per plant or per growing season. Hence increased yield couldaffect the economic benefit one can obtain from the plant in a certaingrowing area and/or growing time.

It should be noted that a plant yield can be affected by variousparameters including, but not limited to, plant biomass; plant vigor;growth rate; seed yield; seed or grain quantity; seed or grain quality;oil yield; content of oil, starch and/or protein in harvested organs(e.g., seeds or vegetative parts of the plant); number of flowers(florets) per panicle (expressed as a ratio of number of filled seedsover number of primary panicles); harvest index; number of plants grownper area; number and size of harvested organs per plant and per area;number of plants per growing area (density); number of harvested organsin field; total leaf area; carbon assimilation and carbon partitioning(the distribution/allocation of carbon within the plant); resistance toshade; number of harvestable organs (e.g. seeds), seeds per pod, weightper seed; and modified architecture [such as increase stalk diameter,thickness or improvement of physical properties (e.g. elasticity)].

As used herein the phrase “seed yield” refers to the number or weight ofthe seeds per plant, seeds per pod, or per growing area or to the weightof a single seed, or to the oil extracted per seed. Hence seed yield canbe affected by seed dimensions (e.g., length, width, perimeter, areaand/or volume), number of (filled) seeds and seed filling rate and byseed oil content. Hence increase seed yield per plant could affect theeconomic benefit one can obtain from the plant in a certain growing areaand/or growing time; and increase seed yield per growing area could beachieved by increasing seed yield per plant, and/or by increasing numberof plants grown on the same given area.

The term “seed” (also referred to as “grain” or “kernel”) as used hereinrefers to a small embryonic plant enclosed in a covering called the seedcoat (usually with some stored food), the product of the ripened ovuleof gymnosperm and angiosperm plants which occurs after fertilization andsome growth within the mother plant.

The phrase “oil content” as used herein refers to the amount of lipidsin a given plant organ, either the seeds (seed oil content) or thevegetative portion of the plant (vegetative oil content) and istypically expressed as percentage of dry weight (10% humidity of seeds)or wet weight (for vegetative portion).

It should be noted that oil content is affected by intrinsic oilproduction of a tissue (e.g., seed, vegetative portion), as well as themass or size of the oil-producing tissue per plant or per growth period.

In one embodiment, increase in oil content of the plant can be achievedby increasing the size/mass of a plant's tissue(s) which comprise oilper growth period. Thus, increased oil content of a plant can beachieved by increasing the yield, growth rate, biomass and vigor of theplant.

As used herein the phrase “plant biomass” refers to the amount (e.g.,measured in grams of air-dry tissue) of a tissue produced from the plantin a growing season, which could also determine or affect the plantyield or the yield per growing area. An increase in plant biomass can bein the whole plant or in parts thereof such as aboveground (harvestable)parts, vegetative biomass, roots and seeds.

As used herein the phrase “growth rate” refers to the increase in plantorgan/tissue size per time (can be measured in cm² per day).

As used herein the phrase “plant vigor” refers to the amount (measuredby weight) of tissue produced by the plant in a given time. Henceincreased vigor could determine or affect the plant yield or the yieldper growing time or growing area. In addition, early vigor (seed and/orseedling) results in improved field stand.

Improving early vigor is an important objective of modern rice breedingprograms in both temperate and tropical rice cultivars. Long roots areimportant for proper soil anchorage in water-seeded rice. Where rice issown directly into flooded fields, and where plants must emerge rapidlythrough water, longer shoots are associated with vigor. Wheredrill-seeding is practiced, longer mesocotyls and coleoptiles areimportant for good seedling emergence. The ability to engineer earlyvigor into plants would be of great importance in agriculture. Forexample, poor early vigor has been a limitation to the introduction ofmaize (Zea mays L.) hybrids based on Corn Belt germplasm in the EuropeanAtlantic.

It should be noted that a plant yield can be determined under stress(e.g., abiotic stress, nitrogen-limiting conditions) and/or non-stress(normal) conditions.

As used herein, the phrase “non-stress conditions” refers to the growthconditions (e.g., water, temperature, light-dark cycles, humidity, saltconcentration, fertilizer concentration in soil, nutrient supply such asnitrogen, phosphorous and/or potassium), that do not significantly gobeyond the everyday climatic and other abiotic conditions that plantsmay encounter, and which allow optimal growth, metabolism, reproductionand/or viability of a plant at any stage in its life cycle (e.g., in acrop plant from seed to a mature plant and back to seed again). Personsskilled in the art are aware of normal soil conditions and climaticconditions for a given plant in a given geographic location. It shouldbe noted that while the non-stress conditions may include some mildvariations from the optimal conditions (which vary from one type/speciesof a plant to another), such variations do not cause the plant to ceasegrowing without the capacity to resume growth.

The phrase “abiotic stress” as used herein refers to any adverse effecton metabolism, growth, reproduction and/or viability of a plant.Accordingly, abiotic stress can be induced by suboptimal environmentalgrowth conditions such as, for example, salinity, water deprivation,flooding, freezing, low or high temperature, heavy metal toxicity,anaerobiosis, nutrient deficiency, atmospheric pollution or UVirradiation. The implications of abiotic stress are discussed in theBackground section.

The phrase “abiotic stress tolerance” as used herein refers to theability of a plant to endure an abiotic stress without suffering asubstantial alteration in metabolism, growth, productivity and/orviability.

Plants are subject to a range of environmental challenges. Several ofthese, including salt stress, general osmotic stress, drought stress andfreezing stress, have the ability to impact whole plant and cellularwater availability. Not surprisingly, then, plant responses to thiscollection of stresses are related. Zhu (2002) Ann. Rev. Plant Biol. 53:247-273 et al. note that “most studies on water stress signaling havefocused on salt stress primarily because plant responses to salt anddrought are closely related and the mechanisms overlap”. Many examplesof similar responses and pathways to this set of stresses have beendocumented. For example, the CBF transcription factors have been shownto condition resistance to salt, freezing and drought (Kasuga et al.(1999) Nature Biotech. 17: 287-291). The Arabidopsis rd29B gene isinduced in response to both salt and dehydration stress, a process thatis mediated largely through an ABA signal transduction process (Uno etal. (2000) Proc. Natl. Acad. Sci. USA 97: 11632-11637), resulting inaltered activity of transcription factors that bind to an upstreamelement within the rd29B promoter. In Mesembryanthemum crystallinum (iceplant), Patharker and Cushman have shown that a calcium-dependentprotein kinase (McCDPKI) is induced by exposure to both drought and saltstresses (Patharker and Cushman (2000) Plant J. 24: 679-691). Thestress-induced kinase was also shown to phosphorylate a transcriptionfactor, presumably altering its activity, although transcript levels ofthe target transcription factor are not altered in response to salt ordrought stress. Similarly, Saijo et al. demonstrated that a ricesalt/drought-induced calmodulin-dependent protein kinase (OsCDPK7)conferred increased salt and drought tolerance to rice whenoverexpressed (Saijo et al. (2000) Plant J. 23: 319-327).

Exposure to dehydration invokes similar survival strategies in plants asdoes freezing stress (see, for example, Yelenosky (1989) Plant Physiol89: 444-451) and drought stress induces freezing tolerance (see, forexample, Siminovitch et al. (1982) Plant Physiol 69: 250-255; and Guy etal. (1992) Planta 188: 265-270). In addition to the induction ofcold-acclimation proteins, strategies that allow plants to survive inlow water conditions may include, for example, reduced surface area, orsurface oil or wax production. In another example increased solutecontent of the plant prevents evaporation and water loss due to heat,drought, salinity, osmoticum, and the like therefore providing a betterplant tolerance to the above stresses.

It will be appreciated that some pathways involved in resistance to onestress (as described above), will also be involved in resistance toother stresses, regulated by the same or homologous genes. Of course,the overall resistance pathways are related, not identical, andtherefore not all genes controlling resistance to one stress willcontrol resistance to the other stresses. Nonetheless, if a geneconditions resistance to one of these stresses, it would be apparent toone skilled in the art to test for resistance to these related stresses.Methods of assessing stress resistance are further provided in theExamples section which follows.

As used herein the phrase “water use efficiency (WUE)” refers to thelevel of organic matter produced per unit of water consumed by theplant, i.e., the dry weight of a plant in relation to the plant's wateruse, e.g., the biomass produced per unit transpiration.

As used herein the phrase “fertilizer use efficiency” refers to themetabolic process(es) which lead to an increase in the plant's yield,biomass, vigor, and growth rate per fertilizer unit applied. Themetabolic process can be the uptake, spread, absorbent, accumulation,relocation (within the plant) and use of one or more of the minerals andorganic moieties absorbed by the plant, such as nitrogen, phosphatesand/or potassium.

As used herein the phrase “fertilizer-limiting conditions” refers togrowth conditions which include a level (e.g., concentration) of afertilizer applied which is below the level needed for normal plantmetabolism, growth, reproduction and/or viability.

As used herein the phrase “nitrogen use efficiency (NUE)” refers to themetabolic process(es) which lead to an increase in the plant's yield,biomass, vigor, and growth rate per nitrogen unit applied. The metabolicprocess can be the uptake, spread, absorbent, accumulation, relocation(within the plant) and use of nitrogen absorbed by the plant.

As used herein the phrase “nitrogen-limiting conditions” refers togrowth conditions which include a level (e.g., concentration) ofnitrogen (e.g., ammonium or nitrate) applied which is below the levelneeded for normal plant metabolism, growth, reproduction and/orviability.

Improved plant NUE and FUE is translated in the field into eitherharvesting similar quantities of yield, while implementing lessfertilizers, or increased yields gained by implementing the same levelsof fertilizers. Thus, improved NUE or FUE has a direct effect on plantyield in the field. Thus, the polynucleotides and polypeptides of someembodiments of the invention positively affect plant yield, seed yield,and plant biomass. In addition, the benefit of improved plant NUE willcertainly improve crop quality and biochemical constituents of the seedsuch as protein yield and oil yield.

It should be noted that improved ABST will confer plants with improvedvigor also under non-stress conditions, resulting in crops havingimproved biomass and/or yield e.g., elongated fibers for the cottonindustry, higher oil content.

The term “fiber” is usually inclusive of thick-walled conducting cellssuch as vessels and tracheids and to fibrillar aggregates of manyindividual fiber cells. Hence, the term “fiber” refers to (a)thick-walled conducting and non-conducting cells of the xylem; (b)fibers of extraxylary origin, including those from phloem, bark, groundtissue, and epidermis; and (c) fibers from stems, leaves, roots, seeds,and flowers or inflorescences (such as those of Sorghum vulgare used inthe manufacture of brushes and brooms).

Example of fiber producing plants, include, but are not limited to,agricultural crops such as cotton, silk cotton tree (Kapok, Ceibapentandra), desert willow, creosote bush, winterfat, balsa, kenaf,roselle, jute, sisal abaca, flax, corn, sugar cane, hemp, ramie, kapok,coir, bamboo, spanish moss and Agave spp. (e.g. sisal).

As used herein the phrase “fiber quality” refers to at least one fiberparameter which is agriculturally desired, or required in the fiberindustry (further described hereinbelow). Examples of such parameters,include but are not limited to, fiber length, fiber strength, fiberfitness, fiber weight per unit length, maturity ratio and uniformity(further described hereinbelow.

Cotton fiber (lint) quality is typically measured according to fiberlength, strength and fineness. Accordingly, the lint quality isconsidered higher when the fiber is longer, stronger and finer.

As used herein the phrase “fiber yield” refers to the amount or quantityof fibers produced from the fiber producing plant.

As used herein the term “increasing” refers to at least about 2%, atleast about 3%, at least about 4%, at least about 5%, at least about10%, at least about 15%, at least about 20%, at least about 30%, atleast about 40%, at least about 50%, at least about 60%, at least about70%, at least about 80%, increase in yield, seed yield, biomass, growthrate, vigor, oil content, fiber yield, fiber quality, abiotic stresstolerance, and/or nitrogen use efficiency of a plant as compared to anative plant [i.e., a plant not modified with the biomolecules(polynucleotide or polypeptides) of the invention, e.g., anon-transformed plant of the same species which is grown under the same(e.g., identical) growth conditions].

The phrase “expressing within the plant an exogenous polynucleotide” asused herein refers to upregulating the expression level of an exogenouspolynucleotide within the plant by introducing the exogenouspolynucleotide into a plant cell or plant and expressing by recombinantmeans, as further described herein below.

As used herein “expressing” refers to expression at the mRNA andoptionally polypeptide level.

As used herein, the phrase “exogenous polynucleotide” refers to aheterologous nucleic acid sequence which may not be naturally expressedwithin the plant or which overexpression in the plant is desired. Theexogenous polynucleotide may be introduced into the plant in a stable ortransient manner, so as to produce a ribonucleic acid (RNA) moleculeand/or a polypeptide molecule. It should be noted that the exogenouspolynucleotide may comprise a nucleic acid sequence which is identicalor partially homologous to an endogenous nucleic acid sequence of theplant.

The term “endogenous” as used herein refers to any polynucleotide orpolypeptide which is present and/or naturally expressed within a plantor a cell thereof.

According to some embodiments of the invention, the exogenouspolynucleotide of the invention comprises a nucleic acid sequenceencoding a polypeptide having an amino acid sequence at least about 80%,at least about 81%, at least about 82%, at least about 83%, at leastabout 84%, at least about 85%, at least about 86%, at least about 87%,at least about 88%, at least about 89%, at least about 90%, at leastabout 91%, at least about 92%, at least about 93%, at least about 94%,at least about 95%, at least about 96%, at least about 97%, at leastabout 98%, at least about 99%, or more say 100% homologous to the aminoacid sequence selected from the group consisting of SEQ ID NOs: 456-774,8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583,12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637,12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695,12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755,12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848,12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895,12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942,12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984,12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016,13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063,13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and14462.

Homology (e.g., percent homology, identity+similarity) can be determinedusing any homology comparison software, including for example, theBlastP or TBLASTN software of the National Center of BiotechnologyInformation (NCBI) such as by using default parameters, when startingfrom a polypeptide sequence; or the tBLASTX algorithm (available via theNCBI) such as by using default parameters, which compares the six-frameconceptual translation products of a nucleotide query sequence (bothstrands) against a protein sequence database.

According to some embodiments of the invention, the term “homology” or“homologous” refers to identity of two or more nucleic acid sequences;or identity of two or more amino acid sequences.

Homologous sequences include both orthologous and paralogous sequences.The term “paralogous” relates to gene-duplications within the genome ofa species leading to paralogous genes. The term “orthologous” relates tohomologous genes in different organisms due to ancestral relationship.

One option to identify orthologues in monocot plant species is byperforming a reciprocal BLAST® search. This may be done by a firstBLAST® involving BLASTing the sequence-of-interest against any sequencedatabase, such as the publicly available NCBI database which may befound at: Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot)nlm (dot) nih (dot) gov. If orthologues in rice were sought, thesequence-of-interest would be BLASTed against, for example, the 28,469full-length cDNA clones from Oryza sativa Nipponbare available at NCBI.The BLAST® results may be filtered. The full-length sequences of eitherthe filtered results or the non-filtered results are then BLASTed back(second BLAST®) against the sequences of the organism from which thesequence-of-interest is derived. The results of the first and secondBLASTs are then compared. An orthologue is identified when the sequenceresulting in the highest score (best hit) in the first BLAST® identifiesin the second BLAST® the query sequence (the originalsequence-of-interest) as the best hit. Using the same rational aparalogue (homolog to a gene in the same organism) is found. In case oflarge sequence families, the ClustalW program may be used [HypertextTransfer Protocol://World WideWeb(dot)ebi(dot)ac(dot)uk/Tools/clustalw2/index(dot)html], followed by aneighbor-joining tree (Hypertext TransferProtocol://en(dot)wikipedia(dot)org/wiki/Neighbor-joining) which helpsvisualizing the clustering.

According to some embodiments of the invention, the exogenouspolynucleotide of the invention encodes a polypeptide having an aminoacid sequence at least about 80%, at least about 81%, at least about82%, at least about 83%, at least about 84%, at least about 85%, atleast about 86%, at least about 87%, at least about 88%, at least about89%, at least about 90%, at least about 91%, at least about 92%, atleast about 93%, at least about 94%, at least about 95%, at least about96%, at least about 97%, at least about 98%, at least about 99%, or moresay 100% identical to the amino acid sequence selected from the groupconsisting of SEQ ID NOs:456-774, 8385-8643, 8645-10650, 10652-10836,10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591,12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666,12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709,12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817,12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859,12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902,12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954,12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994,12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029,13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070,13073-13076, 13079-13084, 13086-14461 and 14462.

According to some embodiments of the invention, the method of increasingyield, biomass, growth rate, vigor, oil content, fiber yield, fiberquality, abiotic stress tolerance, and/or nitrogen use efficiency of aplant is effected by expressing within the plant an exogenouspolynucleotide comprising a nucleic acid sequence encoding a polypeptideat least about 80%, at least about 81%, at least about 82%, at leastabout 83%, at least about 84%, at least about 85%, at least about 86%,at least about 87%, at least about 88%, at least about 89%, at leastabout 90%, at least about 91%, at least about 92%, at least about 93%,at least about 94%, at least about 95%, at least about 96%, at leastabout 97%, at least about 98%, at least about 99%, or more say 100%identical to the amino acid sequence selected from the group consistingof SEQ ID NOs:456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575,12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615,12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677,12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717,12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825,12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886,12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926,12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967,12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003,13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049,13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076,13079-13084, 13086-14461 and 14462, thereby increasing the yield,biomass, growth rate, vigor, oil content, fiber yield, fiber quality,abiotic stress tolerance, and/or nitrogen use efficiency of the plant.

According to some embodiments of the invention, the exogenouspolynucleotide encodes a polypeptide consisting of the amino acidsequence set forth by SEQ ID NO:456-774, 8385-10836, 10838-14461 or14462.

According to an aspect of some embodiments of the invention, the methodof increasing yield, biomass, growth rate, vigor, oil content, fiberyield, fiber quality, abiotic stress tolerance, and/or nitrogen useefficiency of a plant, is effected by expressing within the plant anexogenous polynucleotide comprising a nucleic acid sequence encoding apolypeptide comprising an amino acid sequence selected from the groupconsisting of SEQ ID NOs:456-774, 8385-10836, 10838-14461 and 14462,thereby increasing the yield, biomass, growth rate, vigor, oil content,fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogenuse efficiency of the plant.

According to an aspect of some embodiments of the invention, there isprovided a method of increasing yield, biomass, growth rate, vigor, oilcontent, fiber yield, fiber quality, abiotic stress tolerance, and/ornitrogen use efficiency of a plant, comprising expressing within theplant an exogenous polynucleotide comprising a nucleic acid sequenceencoding a polypeptide selected from the group consisting of SEQ ID NOs:456-774, 8385-10836, 10838-14461 and 14462, thereby increasing theyield, biomass, growth rate, vigor, oil content, fiber yield, fiberquality, abiotic stress tolerance, and/or to nitrogen use efficiency ofthe plant.

According to some embodiments of the invention, the exogenouspolynucleotide encodes a polypeptide consisting of the amino acidsequence set forth by SEQ ID NO: 456-774, 8385-10836, 10838-14461 or14462.

According to some embodiments of the invention the exogenouspolynucleotide comprises a nucleic acid sequence which is at least about80%, at least about 81%, at least about 82%, at least about 83%, atleast about 84%, at least about 85%, at least about 86%, at least about87%, at least about 88%, at least about 89%, at least about 90%, atleast about 91%, at least about 92%, at least about 93%, at least about93%, at least about 94%, at least about 95%, at least about 96%, atleast about 97%, at least about 98%, at least about 99%, e.g., 100%identical to the nucleic acid sequence selected from the groupconsisting of SEQ ID NOs:1-455, 775-6485, 6487-6657, 6660-6664,6666-6701, 6703-6745, 6748-6818, 6820-6821, 6824-6827, 6829-6881, 6883,and 6885-8384.

According to an aspect of some embodiments of the invention, there isprovided a method of increasing yield, biomass, growth rate, vigor, oilcontent, fiber yield, fiber quality, abiotic stress tolerance, and/ornitrogen use efficiency of a plant, comprising expressing within theplant an exogenous polynucleotide comprising a nucleic acid sequence atleast about 80%, at least about 81%, at least about 82%, at least about83%, at least about 84%, at least about 85%, at least about 86%, atleast about 87%, at least about 88%, at least about 89%, at least about90%, at least about 91%, at least about 92%, at least about 93%, atleast about 93%, at least about 94%, at least about 95%, at least about96%, at least about 97%, at least about 98%, at least about 99%, e.g.,100% identical to the nucleic acid sequence selected from the groupconsisting of SEQ ID NOs:1-455, 775-6485, 6487-6657, 6660-6664,6666-6701, 6703-6745, 6748-6818, 6820-6821, 6824-6827, 6829-6881, 6883,and 6885-8384, thereby increasing the yield, biomass, growth rate,vigor, oil content, fiber yield, fiber quality, abiotic stresstolerance, and/or nitrogen use efficiency of the plant.

According to some embodiments of the invention, the homology is a globalhomology, i.e., an homology over the entire amino acid or nucleic acidsequences of the invention and not over portions thereof.

According to some embodiments of the invention, the identity is a globalidentity, i.e., an identity over the entire amino acid or nucleic acidsequences of the invention and not over portions thereof.

Identity (e.g., percent homology) can be determined using any homologycomparison software, including for example, the BlastN software of theNational Center of Biotechnology Information (NCBI) such as by usingdefault parameters.

According to some embodiments of the invention the exogenouspolynucleotide is at least about 80%, at least about 81%, at least about82%, at least about 83%, at least about 84%, at least about 85%, atleast about 86%, at least about 87%, at least about 88%, at least about89%, at least about 90%, at least about 91%, at least about 92%, atleast about 93%, at least about 93%, at least about 94%, at least about95%, at least about 96%, at least about 97%, at least about 98%, atleast about 99%, e.g., 100% identical to the polynucleotide selectedfrom the group consisting of SEQ ID NOs:1-455, 775-6485, 6487-6657,6660-6664, 6666-6701, 6703-6745, 6748-6818, 6820-6821, 6824-6827,6829-6881, 6883, and 6885-8384.

According to some embodiments of the invention the exogenouspolynucleotide is set forth by SEQ ID NO:1-455, 775-8383 or 8384.

As used herein the term “polynucleotide” refers to a single or doublestranded nucleic acid sequence which is isolated and provided in theform of an RNA sequence, a complementary polynucleotide sequence (cDNA),a genomic polynucleotide sequence and/or a composite polynucleotidesequences (e.g., a combination of the above).

The term “isolated” refers to at least partially separated from thenatural environment e.g., from a plant cell.

As used herein the phrase “complementary polynucleotide sequence” refersto a sequence, which results from reverse transcription of messenger RNAusing a reverse transcriptase or any other RNA dependent DNA polymerase.Such a sequence can be subsequently amplified in vivo or in vitro usinga DNA dependent DNA polymerase.

As used herein the phrase “genomic polynucleotide sequence” refers to asequence derived (isolated) from a chromosome and thus it represents acontiguous portion of a chromosome.

As used herein the phrase “composite polynucleotide sequence” refers toa sequence, which is at least partially complementary and at leastpartially genomic. A composite sequence can include some exonalsequences required to encode the polypeptide of the present invention,as well as some intronic sequences interposing therebetween. Theintronic sequences can be of any source, including of other genes, andtypically will include conserved splicing signal sequences. Suchintronic sequences may further include cis acting expression regulatoryelements.

According to an aspect of some embodiments of the invention, there isprovided a method of increasing fertilizer use efficiency (e.g.,nitrogen use efficiency) and/or oil content of a plant, comprisingexpressing within the plant an exogenous polynucleotide comprising anucleic acid sequence encoding a polypeptide at least about 80%, atleast about 81%, at least about 82%, at least about 83%, at least about84%, at least about 85%, at least about 86%, at least about 87%, atleast about 88%, at least about 89%, at least about 90%, at least about91%, at least about 92%, at least about 93%, at least about 94%, atleast about 95%, at least about 96%, at least about 97%, at least about98%, at least about 99%, or more say 100% homologous to the amino acidsequence set forth in SEQ ID NO: 10837, thereby increasing thefertilizer use efficiency (e.g., nitrogen use efficiency) and/or oilcontent of the plant.

According to an aspect of some embodiments of the invention, the methodof increasing fertilizer use efficiency (e.g., nitrogen use efficiency)and/or oil content of a plant is effected by expressing within the plantan exogenous polynucleotide comprising a nucleic acid sequence encodingthe polypeptide set forth in SEQ ID NO: 10837, thereby increasing thefertilizer use efficiency (e.g., nitrogen use efficiency) and/or oilcontent of a plant.

According to some embodiments of the invention, the exogenouspolynucleotide encodes a polypeptide consisting of the amino acidsequence set forth by SEQ ID NO: 10837.

Nucleic acid sequences encoding the polypeptides of the presentinvention may be optimized for expression. Examples of such sequencemodifications include, but are not limited to, an altered G/C content tomore closely approach that typically found in the plant species ofinterest, and the removal of codons atypically found in the plantspecies commonly referred to as codon optimization.

The phrase “codon optimization” refers to the selection of appropriateDNA nucleotides for use within a structural gene or fragment thereofthat approaches codon usage within the plant of interest. Therefore, anoptimized gene or nucleic acid sequence refers to a gene in which thenucleotide sequence of a native or naturally occurring gene has beenmodified in order to utilize statistically-preferred orstatistically-favored codons within the plant. The nucleotide sequencetypically is examined at the DNA level and the coding region optimizedfor expression in the plant species determined using any suitableprocedure, for example as described in Sardana et al. (1996, Plant CellReports 15:677-681). In this method, the standard deviation of codonusage, a measure of codon usage bias, may be calculated by first findingthe squared proportional deviation of usage of each codon of the nativegene relative to that of highly expressed plant genes, followed by acalculation of the average squared deviation. The formula used is: 1SDCU=n=1 N[(Xn−Yn)/Yn]2/N, where Xn refers to the frequency of usage ofcodon n in highly expressed plant genes, where Yn to the frequency ofusage of codon n in the gene of interest and N refers to the totalnumber of codons in the gene of interest. A Table of codon usage fromhighly expressed genes of dicotyledonous plants is compiled using thedata of Murray et al. (1989, Nuc Acids Res. 17:477-498).

One method of optimizing the nucleic acid sequence in accordance withthe preferred codon usage for a particular plant cell type is based onthe direct use, without performing any extra statistical calculations,of codon optimization Tables such as those provided on-line at the CodonUsage Database through the NIAS (National Institute of AgrobiologicalSciences) DNA bank in Japan (Hypertext Transfer Protocol://World WideWeb (dot) kazusa (dot) or (dot) jp/codon/). The Codon Usage Databasecontains codon usage tables for a number of different species, with eachcodon usage Table having been statistically determined based on the datapresent in Genbank.

By using the above Tables to determine the most preferred or mostfavored codons for each amino acid in a particular species (for example,rice), a naturally-occurring nucleotide sequence encoding a protein ofinterest can be codon optimized for that particular plant species. Thisis effected by replacing codons that may have a low statisticalincidence in the particular species genome with corresponding codons, inregard to an amino acid, that are statistically more favored. However,one or more less-favored codons may be selected to delete existingrestriction sites, to create new ones at potentially useful junctions(5′ and 3′ ends to add signal peptide or termination cassettes, internalsites that might be used to cut and splice segments together to producea correct full-length sequence), or to eliminate nucleotide sequencesthat may negatively effect mRNA stability or expression.

The naturally-occurring encoding nucleotide sequence may already, inadvance of any modification, contain a number of codons that correspondto a statistically-favored codon in a particular plant species.Therefore, codon optimization of the native nucleotide sequence maycomprise determining which codons, within the native nucleotidesequence, are not statistically-favored with regards to a particularplant, and modifying these codons in accordance with a codon usage tableof the particular plant to produce a codon optimized derivative. Amodified nucleotide sequence may be fully or partially optimized forplant codon usage provided that the protein encoded by the modifiednucleotide sequence is produced at a level higher than the proteinencoded by the corresponding naturally occurring or native gene.Construction of synthetic genes by altering the codon usage is describedin for example PCT Patent Application 93/07278.

According to some embodiments of the invention, the exogenouspolynucleotide is a non-coding RNA.

As used herein the phrase ‘non-coding RNA” refers to an RNA moleculewhich does not encode an amino acid sequence (a polypeptide). Examplesof such non-coding RNA molecules include, but are not limited to, anantisense RNA, a pre-miRNA (precursor of a microRNA), or a precursor ofa Piwi-interacting RNA (piRNA).

Non-limiting examples of non-coding RNA polynucleotides are provided inSEQ ID NOs: 201, 258, 455, 1269, 1312, 2017, 2174, 2278, 2289, 2564,2565, 2641, 2642, 2643, 2799, 2827, 2828, 2829, 2830, 2835, 2836, 2837,2852, 2853, 2873, 2877, 3026, 3181, 3250, 3311, 3466, 3480, 4017, 4243,4339, 4346, 4347, 4508, 4509, 4540, 4541, 4546, 4547, 4548, 4563, 4564,4565, 4569, 4570, 4581, 4906, 5530, 5955, 5979, 6033, and 6868.

Thus, the invention encompasses nucleic acid sequences describedhereinabove; fragments thereof, sequences hybridizable therewith,sequences homologous thereto, sequences encoding similar polypeptideswith different codon usage, altered sequences characterized bymutations, such as deletion, insertion or substitution of one or morenucleotides, either naturally occurring or man induced, either randomlyor in a targeted fashion.

The invention provides an isolated polynucleotide comprising a nucleicacid sequence at least about 80%, at least about 81%, at least about82%, at least about 83%, at least about 84%, at least about 85%, atleast about 86%, at least about 87%, at least about 88%, at least about89%, at least about 90%, at least about 91%, at least about 92%, atleast about 93%, at least about 93%, at least about 94%, at least about95%, at least about 96%, at least about 97%, at least about 98%, atleast about 99%, e.g., 100% identical to the polynucleotide selectedfrom the group consisting of SEQ ID NOs:1-455, 775-6485, 6487-6657,6660-6664, 6666-6701, 6703-6745, 6748-6818, 6820-6821, 6824-6827,6829-6881, 6883, and 6885-8384.

According to some embodiments of the invention the nucleic acid sequenceis capable of increasing yield, growth rate, vigor, biomass, oilcontent, fiber yield, fiber quality, nitrogen use efficiency, fertilizeruse efficiency, abiotic stress tolerance and/or water use efficiency ofa plant.

According to some embodiments of the invention the isolatedpolynucleotide comprising the nucleic acid sequence selected from thegroup consisting of SEQ ID NOs: 1-455, 775-8383 and 8384.

According to some embodiments of the invention the isolatedpolynucleotide is set forth by SEQ ID NO:1-455, 775-8383 or 8384.

The invention provides an isolated polynucleotide comprising a nucleicacid sequence encoding a polypeptide which comprises an amino acidsequence at least about 80%, at least about 81%, at least about 82%, atleast about 83%, at least about 84%, at least about 85%, at least about86%, at least about 87%, at least about 88%, at least about 89%, atleast about 90%, at least about 91%, at least about 92%, at least about93%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or more say 100% homologous to the amino acid sequence selectedfrom the group consisting of SEQ ID NOs: 456-774, 8385-8643, 8645-10650,10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590,12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666,12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709,12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817,12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859,12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902,12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954,12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994,12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029,13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070,13073-13076, 13079-13084, 13086-14461 and 14462.

According to some embodiments of the invention the amino acid sequenceis capable of increasing yield, growth rate, vigor, biomass, oilcontent, fiber yield, fiber quality, nitrogen use efficiency, fertilizeruse efficiency, abiotic stress tolerance and/or water use efficiency ofa plant.

The invention provides an isolated polynucleotide comprising a nucleicacid sequence encoding a polypeptide which comprises the amino acidsequence selected from the group consisting of SEQ ID NOs: 456-774,8385-10836, 10838-14461 and 14462.

According to an aspect of some embodiments of the invention, there isprovided a nucleic acid construct comprising the isolated polynucleotideof the invention, and a promoter for directing transcription of thenucleic acid sequence in a host cell.

The invention provides an isolated polypeptide comprising an amino acidsequence at least about 80%, at least about 81%, at least about 82%, atleast about 83%, at least about 84%, at least about 85%, at least about86%, at least about 87%, at least about 88%, at least about 89%, atleast about 90%, at least about 91%, at least about 92%, at least about93%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or more say 100% homologous to an amino acid sequence selected fromthe group consisting of SEQ ID NOs: 456-774, 8385-8643, 8645-10650,10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590,12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666,12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709,12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817,12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859,12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902,12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954,12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994,12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029,13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070,13073-13076, 13079-13084, 13086-14461 and 14462.

According to some embodiments of the invention, the polypeptidecomprising an amino acid sequence selected from the group consisting ofSEQ ID NOs: 456-774, 8385-10836, 10838-14461 and 14462.

According to some embodiments of the invention, the polypeptide is setforth by SEQ ID NO: 456-774, 8385-10836, 10838-14461 or 14462.

The invention also encompasses fragments of the above describedpolypeptides and polypeptides having mutations, such as deletions,insertions or substitutions of one or more amino acids, either naturallyoccurring or man induced, either randomly or in a targeted fashion.

The term “‘plant” as used herein encompasses whole plants, ancestors andprogeny of the plants and plant parts, including seeds, shoots, stems,roots (including tubers), and plant cells, tissues and organs. The plantmay be in any form including suspension cultures, embryos, meristematicregions, callus tissue, leaves, gametophytes, sporophytes, pollen, andmicrospores. Plants that are particularly useful in the methods of theinvention include all plants which belong to the superfamilyViridiplantae, in particular monocotyledonous and dicotyledonous plantsincluding a fodder or forage legume, ornamental plant, food crop, tree,or shrub selected from the list comprising Acacia spp., Acer spp.,Actinidia spp., Aesculus spp., Agathis australis, Albizia amara,Alsophila tricolor. Andropogon spp., Arachis spp, Areca catechu, Asteliafragrans, Astragalus cicer, Baikiaea plurijuga, Betula spp., Brassicaspp., Bruguiera gymnorrhiza, Burkea africana, Butea frondosa, Cadabafarinosa, Calliandra spp, Camellia sinensis, Canna indica, Capsicumspp., Cassia spp., Centroema pubescens, Chacoomeles spp., Cinnamomumcassia, Coffea arabica, Colophospermum mopane, Coronillia varia,Cotoneaster serotina, Crataegus spp., Cucumis spp., Cupressus spp.,Cyathea dealbata, Cydonia oblonga, Cryptomeria japonica, Cymbopogonspp., Cynthea dealbata, Cydonia oblonga, Dalbergia monetaria, Davalliadivaricata, Desmodium spp., Dicksonia squarosa, Dibeteropogonamplectens, Dioclea spp, Dolichos spp., Dorycnium rectum, Echinochloapyramidalis, Ehraffia spp., Eleusine coracana, Eragrestis spp.,Erythrina spp., Eucalypfus spp., Euclea schimperi, Eulalia vi/losa,Pagopyrum spp., Feijoa sellowlana, Fragaria spp., Flemingia spp,Freycinetia banksli, Geranium thunbergii, GinAgo biloba, Glycinejavanica, Gliricidia spp, Gossypium hirsutum, Grevillea spp., Guibourtiacoleosperma, Hedysarum spp., Hemaffhia altissima, Heteropogon contoffus,Hordeum vulgare, Hyparrhenia rufa, Hypericum erectum, Hypeffheliadissolute, Indigo incamata, Iris spp., Leptarrhena pyrolifolia,Lespediza spp., Lettuca spp., Leucaena leucocephala, Loudetia simplex,Lotonus bainesli, Lotus spp., Macrotyloma axillare, Malus spp., Manihotesculenta, Medicago saliva, Metasequoia glyptostroboides, Musasapientum, Nicotianum spp., Onobrychis spp., Ornithopus spp., Oryzaspp., Peltophorum africanum, Pennisetum spp., Persea gratissima, Petuniaspp., Phaseolus spp., Phoenix canariensis, Phormium cookianum, Photiniaspp., Picea glauca, Pinus spp., Pisum sativam, Podocarpus totara,Pogonarthria fleckii, Pogonaffhria squarrosa, Populus spp., Prosopiscineraria, Pseudotsuga menziesii, Pterolobium stellatum, Pyrus communis,Quercus spp., Rhaphiolepsis umbellata, Rhopalostylis sapida, Rhusnatalensis, Ribes grossularia, Ribes spp., Robinia pseudoacacia, Rosaspp., Rubus spp., Salix spp., Schyzachyrium sanguineum, Sciadopitysvefficillata, Sequoia sempervirens, Sequoiadendron giganteum, Sorghumbicolor, Spinacia spp., Sporobolus fimbriatus, Stiburus alopecuroides,Stylosanthos humilis, Tadehagi spp, Taxodium distichum, Themedatriandra, Trifolium spp., Triticum spp., Tsuga heterophylla, Vacciniumspp., Vicia spp., Vitis vinifera, Watsonia pyramidata, Zantedeschiaaethiopica, Zea mays, amaranth, artichoke, asparagus, broccoli, Brusselssprouts, cabbage, canola, carrot, cauliflower, celery, collard greens,flax, kale, lentil, oilseed rape, okra, onion, potato, rice, soybean,straw, sugar beet, sugar cane, sunflower, tomato, squash tea, maize,wheat, barely, rye, oat, peanut, pea, lentil and alfalfa, cotton,rapeseed, canola, pepper, sunflower, tobacco, eggplant, eucalyptus, atree, an ornamental plant, a perennial grass and a forage crop.Alternatively algae and other non-Viridiplantae can be used for themethods of the present invention.

According to some embodiments of the invention, the plant used by themethod of the invention is a crop plant such as rice, maize, wheat,barley, peanut, potato, sesame, olive tree, palm oil, banana, soybean,sunflower, canola, sugarcane, alfalfa, millet, leguminosae (bean, pea),flax, lupinus, rapeseed, tobacco, poplar and cotton.

According to some embodiments of the invention the plant is adicotyledonous plant.

According to some embodiments of the invention the plant is amonocotyledonous plant.

According to some embodiments of the invention, there is provided aplant cell exogenously expressing the polynucleotide of some embodimentsof the invention, the nucleic acid construct of some embodiments of theinvention and/or the polypeptide of some embodiments of the invention.

According to some embodiments of the invention, expressing the exogenouspolynucleotide of the invention within the plant is effected bytransforming one or more cells of the plant with the exogenouspolynucleotide, followed by generating a mature plant from thetransformed cells and cultivating the mature plant under conditionssuitable for expressing the exogenous polynucleotide within the matureplant.

According to some embodiments of the invention, the transformation iseffected by introducing to the plant cell a nucleic acid construct whichincludes the exogenous polynucleotide of some embodiments of theinvention and at least one promoter for directing transcription of theexogenous polynucleotide in a host cell (a plant cell). Further detailsof suitable transformation approaches are provided hereinbelow.

As mentioned, the nucleic acid construct according to some embodimentsof the invention comprises a promoter sequence and the isolatedpolynucleotide of the invention.

According to some embodiments of the invention, the isolatedpolynucleotide is operably linked to the promoter sequence.

A coding nucleic acid sequence is “operably linked” to a regulatorysequence (e.g., promoter) if the regulatory sequence is capable ofexerting a regulatory effect on the coding sequence linked thereto.

As used herein, the term “promoter” refers to a region of DNA which liesupstream of the transcriptional initiation site of a gene to which RNApolymerase binds to initiate transcription of RNA. The promoter controlswhere (e.g., which portion of a plant) and/or when (e.g., at which stageor condition in the lifetime of an organism) the gene is expressed.

According to some embodiments of the invention, the promoter isheterologous to the isolated polynucleotide and/or to the host cell.

Any suitable promoter sequence can be used by the nucleic acid constructof the present invention. Preferably the promoter is a constitutivepromoter, a tissue-specific, or an abiotic stress-inducible promoter.

According to some embodiments of the invention, the promoter is a plantpromoter, which is suitable for expression of the exogenouspolynucleotide in a plant cell.

Suitable constitutive promoters include, for example, CaMV 35S promoter[SEQ ID NO:14463 (pQFNC); SEQ ID NO:14464 (PJJ 35S from Brachypodium);SEQ ID NO:14465 (Odell et al., Nature 313:810-812, 1985)], ArabidopsisAt6669 promoter (SEQ ID NO:14466; see PCT Publication No. WO04081173A2or the new At6669 promoter (SEQ ID NO:14467); maize Ubi 1 (maizepolyubiquitin-1, SEQ ID NO:14468; Christensen et al., Plant Sol. Biol.18:675-689, 1992; Taylor et al., Plant Cell Rep 12:491-495, 1993); riceactin 1 (SEQ ID NO:14469, McElroy et al., Plant Cell 2:163-171, 1990);pEMU (Last et al., Theor. Appl. Genet. 81:581-588, 1991); CaMV 19S(Nilsson et al., Physiol. Plant 100:456-462, 1997); GOS2 (SEQ IDNO:14470, de Pater et al, Plant J November; 2(6):837-44, 1992); Ubi Ipromoter (SEQ ID NO:14471); RBCS promoter (SEQ ID NO:14472); Ricecyclophilin (Bucholz et al, Plant Mol Biol. 25(5):837-43, 1994); MaizeH3 histone (Lepetit et al, Mol. Gen. Genet. 231: 276-285, 1992); Actin 2(An et al, Plant J. 10(1); 107-121, 1996) and Synthetic Super MAS (Ni etal., The Plant Journal 7: 661-76, 1995). Other constitutive promotersinclude those in U.S. Pat. Nos. 5,659,026, 5,608,149; 5,608,144;5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; and 5,608,142.

Suitable tissue-specific promoters include, but not limited to,leaf-specific promoters [e.g., AT5G06690 (Thioredoxin) (high expression,SEQ ID NO:14473), AT5G61520 (AtSTP3) (low expression, SEQ ID NO:14474)described in Buttner et al 2000 Plant, Cell and Environment 23, 175-184,or the promoters described in Yamamoto et al., Plant J. 12:255-265,1997; Kwon et al., Plant Physiol. 105:357-67, 1994; Yamamoto et al.,Plant Cell Physiol. 35:773-778, 1994; Gotor et al., Plant J. 3:509-18,1993; Orozco et al., Plant Mol. Biol. 23:1129-1138, 1993; and Matsuokaet al., Proc. Natl. Acad. Sci. USA 90:9586-9590, 1993; as well asArabidopsis STP3 (AT5G61520) promoter (Buttner et al., Plant, Cell andEnvironment 23:175-184, 2000)], seed-preferred promoters [e.g., Napin(originated from Brassica napus which is characterized by a seedspecific promoter activity; Stuitje A. R. et. al. Plant BiotechnologyJournal 1 (4): 301-309; SEQ ID NO:14475 from seed specific genes (Simon,et al., Plant Mol. Biol. 5. 191, 1985; Scofield, et al., J. Biol. Chem.262: 12202, 1987; Baszczynski, et al., Plant Mol. Biol. 14: 633, 1990),rice PG5a (U.S. Pat. No. 7,700,835), early seed development ArabidopsisBAN (SEQ ID NO:14476, US 2009/0031450 A1), late seed developmentArabidopsis ABI3 (SEQ ID NO:14477) (Ng et al., Plant Molecular Biology54: 25-38, 2004), Brazil Nut albumin (Pearson et al., Plant Mol. Biol.18: 235-245, 1992), legumin (Ellis, et al. Plant Mol. Biol. 10: 203-214,1988), Glutelin (rice) (Takaiwa, et al., Mol. Gen. Genet. 208: 15-22,1986; Takaiwa, et al., FEBS Letts. 221: 43-47, 1987), Zein (Matzke et alPlant Mol Biol, 143).323-32 1990), napA (Stalberg, et al, Planta 199:515-519, 1996), Wheat SPA (Albani et al, Plant Cell, 9: 171-184, 1997),sunflower oleosin (Cummins, et al., Plant Mol. Biol. 19: 873-876,1992)], endosperm specific promoters [e.g., wheat LMW and HMW,glutenin-1 (Thomas and Flavell, The Plant Cell 2:1171-1180, 1990; MolGen Genet 216:81-90, 1989; NAR 17:461-2), wheat a, b and g gliadins(EMBO3:1409-15, 1984), Barley ltrl promoter, barley B1, C, D hordein(Theor Appl Gen 98:1253-62, 1999; Plant J 4:343-55, 1993; Mol Gen Genet250:750-60, 1996), Barley DOF (Mena et al, The Plant Journal, 116(1):53-62, 1998), Biz2 (EP99106056.7), Barley SS2 (Guerin and CarboneroPlant Physiology 114: 1 55-62, 1997), wheat Tarp60 (Kovalchuk et al.,Plant Mol Biol 71:81-98, 2009), barley D-hordein (D-Hor) and B-hordein(B-Hor) (Agnelo Furtado, Robert J. Henry and Alessandro Pellegrineschi(2009)], Synthetic promoter (Vicente-Carbajosa et al., Plant J. 13:629-640, 1998), rice prolamin NRP33, rice-globulin Glb-1 (Wu et al,Plant Cell Physiology 39(8) 885-889, 1998), rice alpha-globulinREB/OHP-1 (Nakase et al. Plant Mol. Biol. 33: 513-S22, 1997), riceADP-glucose PP (Trans Res 6:157-68, 1997), maize ESR gene family (PlantJ 12:235-46, 1997), sorgum gamma-kafirin (PMB 32:1029-35, 1996)], embryospecific promoters [e.g., rice OSH1 (Sato et al, Proc. Natl. Acad. Sci.USA, 93: 8117-8122), KNOX (Postma-Haarsma ef al, Plant Mol. Biol.39:257-71, 1999), rice oleosin (Wu et at, J. Biochem., 123:386, 1998)],and flower-specific promoters [e.g., AtPRP4, chalene synthase (chsA)(Van der Meer, et al., Plant Mol. Biol. 15, 95-109, 1990), LAT52 (Twellet al Mol. Gen Genet. 217:240-245; 1989), Arabidopsis apetala-3 (Tillyet al., Development. 125:1647-57, 1998), Arabidopsis APETALA 1(AT1G69120, API) (SEQ ID NO:14478) (Hempel et al., Development124:3845-3853, 1997)], and root promoters [e.g., the ROOTP promoter [SEQID NO: 14479]; rice ExpB5 and barley ExpB1 promoters (Won et al. Mol.Cells 30: 369-376, 2010); arabidopsis monoterpene synthase (AT3G25820)promoter (Chen et al., Plant Phys 135:1956-66, 2004); arabidopsis Pho1promoter (SEQ ID NO:14480, Hamburger et al., Plant Cell. 14: 889-902,2002), which is also slightly induced Pi stress].

Suitable abiotic stress-inducible promoters include, but not limited to,salt-inducible promoters such as RD29A (Yamaguchi-Shinozalei et al.,Mol. Gen. Genet. 236:331-340, 1993); drought-inducible promoters such asmaize rab17 gene promoter (Pla et. al., Plant Mol. Biol. 21:259-266,1993), maize rab28 gene promoter (Busk et. al., Plant J. 11:1285-1295,1997) and maize Ivr2 gene promoter (Pelleschi et. al., Plant Mol. Biol.39:373-380, 1999); heat-inducible promoters such as heat tomatohsp80-promoter from tomato (U.S. Pat. No. 5,187,267).

The nucleic acid construct of some embodiments of the invention canfurther include an appropriate selectable marker and/or an origin ofreplication. According to some embodiments of the invention, the nucleicacid construct utilized is a shuttle vector, which can propagate both inE. coli (wherein the construct comprises an appropriate selectablemarker and origin of replication) and be compatible with propagation incells. The construct according to the present invention can be, forexample, a plasmid, a bacmid, a phagemid, a cosmid, a phage, a virus oran artificial chromosome.

The nucleic acid construct of some embodiments of the invention can beutilized to stably or transiently transform plant cells. In stabletransformation, the exogenous polynucleotide is integrated into theplant genome and as such it represents a stable and inherited trait. Intransient transformation, the exogenous polynucleotide is expressed bythe cell transformed but it is not integrated into the genome and assuch it represents a transient trait.

There are various methods of introducing foreign genes into bothmonocotyledonous and dicotyledonous plants (Potrykus, I., Annu. Rev.Plant. Physiol., Plant. Mol. Biol. (1991) 42:205-225; Shimamoto et al.,Nature (1989) 338:274-276).

The principle methods of causing stable integration of exogenous DNAinto plant genomic DNA include two main approaches:

(i) Agrobacterium-mediated gene transfer: Klee et al. (1987) Annu. Rev.Plant Physiol. 38:467-486; Klee and Rogers in Cell Culture and SomaticCell Genetics of Plants, Vol. 6, Molecular Biology of Plant NuclearGenes, eds. Schell, J., and Vasil, L. K., Academic Publishers, SanDiego, Calif. (1989) p. 2-25; Gatenby, in Plant Biotechnology, eds.Kung, S. and Arntzen, C. J., Butterworth Publishers, Boston, Mass.(1989) p. 93-112.

(ii) Direct DNA uptake: Paszkowski et al., in Cell Culture and SomaticCell Genetics of Plants, Vol. 6, Molecular Biology of Plant NuclearGenes eds. Schell, J., and Vasil, L. K., Academic Publishers, San Diego,Calif. (1989) p. 52-68; including methods for direct uptake of DNA intoprotoplasts, Toriyama, K. et al. (1988) Bio/Technology 6:1072-1074. DNAuptake induced by brief electric shock of plant cells: Zhang et al.Plant Cell Rep. (1988) 7:379-384. Fromm et al. Nature (1986)319:791-793. DNA injection into plant cells or tissues by particlebombardment, Klein et al. Bio/Technology (1988) 6:559-563; McCabe et al.Bio/Technology (1988) 6:923-926; Sanford, Physiol. Plant. (1990)79:206-209; by the use of micropipette systems: Neuhaus et al., Theor.Appl. Genet. (1987) 75:30-36; Neuhaus and Spangenberg, Physiol. Plant.(1990) 79:213-217; glass fibers or silicon carbide whiskertransformation of cell cultures, embryos or callus tissue, U.S. Pat. No.5,464,765 or by the direct incubation of DNA with germinating pollen,DeWet et al. in Experimental Manipulation of Ovule Tissue, eds. Chapman,G. P. and Mantell, S. H. and Daniels, W. Longman, London, (1985) p.197-209; and Ohta, Proc. Natl. Acad. Sci. USA (1986) 83:715-719.

The Agrobacterium system includes the use of plasmid vectors thatcontain defined DNA segments that integrate into the plant genomic DNA.Methods of inoculation of the plant tissue vary depending upon the plantspecies and the Agrobacterium delivery system. A widely used approach isthe leaf disc procedure which can be performed with any tissue explantthat provides a good source for initiation of whole plantdifferentiation. See, e.g., Horsch et al. in Plant Molecular BiologyManual A5, Kluwer Academic Publishers, Dordrecht (1988) p. 1-9. Asupplementary approach employs the Agrobacterium delivery system incombination with vacuum infiltration. The Agrobacterium system isespecially viable in the creation of transgenic dicotyledonous plants.

There are various methods of direct DNA transfer into plant cells. Inelectroporation, the protoplasts are briefly exposed to a strongelectric field. In microinjection, the DNA is mechanically injecteddirectly into the cells using very small micropipettes. In microparticlebombardment, the DNA is adsorbed on microprojectiles such as magnesiumsulfate crystals or tungsten particles, and the microprojectiles arephysically accelerated into cells or plant tissues.

Following stable transformation plant propagation is exercised. The mostcommon method of plant propagation is by seed. Regeneration by seedpropagation, however, has the deficiency that due to heterozygositythere is a lack of uniformity in the crop, since seeds are produced byplants according to the genetic variances governed by Mendelian rules.Basically, each seed is genetically different and each will grow withits own specific traits. Therefore, it is preferred that the transformedplant be produced such that the regenerated plant has the identicaltraits and characteristics of the parent transgenic plant. Therefore, itis preferred that the transformed plant be regenerated bymicropropagation which provides a rapid, consistent reproduction of thetransformed plants.

Micropropagation is a process of growing new generation plants from asingle piece of tissue that has been excised from a selected parentplant or cultivar. This process permits the mass reproduction of plantshaving the preferred tissue expressing the fusion protein. The newgeneration plants which are produced are genetically identical to, andhave all of the characteristics of, the original plant. Micropropagationallows mass production of quality plant material in a short period oftime and offers a rapid multiplication of selected cultivars in thepreservation of the characteristics of the original transgenic ortransformed plant. The advantages of cloning plants are the speed ofplant multiplication and the quality and uniformity of plants produced.

Micropropagation is a multi-stage procedure that requires alteration ofculture medium or growth conditions between stages. Thus, themicropropagation process involves four basic stages: Stage one, initialtissue culturing; stage two, tissue culture multiplication; stage three,differentiation and plant formation; and stage four, greenhouseculturing and hardening. During stage one, initial tissue culturing, thetissue culture is established and certified contaminant-free. Duringstage two, the initial tissue culture is multiplied until a sufficientnumber of tissue samples are produced to meet production goals. Duringstage three, the tissue samples grown in stage two are divided and growninto individual plantlets. At stage four, the transformed plantlets aretransferred to a greenhouse for hardening where the plants' tolerance tolight is gradually increased so that it can be grown in the naturalenvironment.

According to some embodiments of the invention, the transgenic plantsare generated by transient transformation of leaf cells, meristematiccells or the whole plant.

Transient transformation can be effected by any of the direct DNAtransfer methods described above or by viral infection using modifiedplant viruses.

Viruses that have been shown to be useful for the transformation ofplant hosts include CaMV, Tobacco mosaic virus (TMV), brome mosaic virus(BMV) and Bean Common Mosaic Virus (BV or BCMV). Transformation ofplants using plant viruses is described in U.S. Pat. No. 4,855,237 (beangolden mosaic virus; BGV), EP-A 67,553 (TMV), Japanese PublishedApplication No. 63-14693 (TMV), EPA 194,809 (BV), EPA 278,667 (BV); andGluzman, Y. et al., Communications in Molecular Biology: Viral Vectors,Cold Spring Harbor Laboratory, New York, pp. 172-189 (1988). Pseudovirusparticles for use in expressing foreign DNA in many hosts, includingplants are described in WO 87/06261.

According to some embodiments of the invention, the virus used fortransient transformations is avirulent and thus is incapable of causingsevere symptoms such as reduced growth rate, mosaic, ring spots, leafroll, yellowing, streaking, pox formation, tumor formation and pitting.A suitable avirulent virus may be a naturally occurring avirulent virusor an artificially attenuated virus. Virus attenuation may be effectedby using methods well known in the art including, but not limited to,sub-lethal heating, chemical treatment or by directed mutagenesistechniques such as described, for example, by Kurihara and Watanabe(Molecular Plant Pathology 4:259-269, 2003), Gal-on et al. (1992),Atreya et al. (1992) and Huet et al. (1994).

Suitable virus strains can be obtained from available sources such as,for example, the American Type culture Collection (ATCC) or by isolationfrom infected plants. Isolation of viruses from infected plant tissuescan be effected by techniques well known in the art such as described,for example by Foster and Tatlor, Eds. “Plant Virology Protocols: FromVirus Isolation to Transgenic Resistance (Methods in Molecular Biology(Humana Pr), Vol 81)”, Humana Press, 1998. Briefly, tissues of aninfected plant believed to contain a high concentration of a suitablevirus, preferably young leaves and flower petals, are ground in a buffersolution (e.g., phosphate buffer solution) to produce a virus infectedsap which can be used in subsequent inoculations.

Construction of plant RNA viruses for the introduction and expression ofnon-viral exogenous polynucleotide sequences in plants is demonstratedby the above references as well as by Dawson, W. O. et al., Virology(1989) 172:285-292; Takamatsu et al. EMBO J. (1987) 6:307-311; French etal. Science (1986) 231:1294-1297; Takamatsu et al. FEBS Letters (1990)269:73-76; and U.S. Pat. No. 5,316,931.

When the virus is a DNA virus, suitable modifications can be made to thevirus itself. Alternatively, the virus can first be cloned into abacterial plasmid for ease of constructing the desired viral vector withthe foreign DNA. The virus can then be excised from the plasmid. If thevirus is a DNA virus, a bacterial origin of replication can be attachedto the viral DNA, which is then replicated by the bacteria.Transcription and translation of this DNA will produce the coat proteinwhich will encapsidate the viral DNA. If the virus is an RNA virus, thevirus is generally cloned as a cDNA and inserted into a plasmid. Theplasmid is then used to make all of the constructions. The RNA virus isthen produced by transcribing the viral sequence of the plasmid andtranslation of the viral genes to produce the coat protein(s) whichencapsidate the viral RNA.

In one embodiment, a plant viral polynucleotide is provided in which thenative coat protein coding sequence has been deleted from a viralpolynucleotide, a non-native plant viral coat protein coding sequenceand a non-native promoter, preferably the subgenomic promoter of thenon-native coat protein coding sequence, capable of expression in theplant host, packaging of the recombinant plant viral polynucleotide, andensuring a systemic infection of the host by the recombinant plant viralpolynucleotide, has been inserted. Alternatively, the coat protein genemay be inactivated by insertion of the non-native polynucleotidesequence within it, such that a protein is produced. The recombinantplant viral polynucleotide may contain one or more additional non-nativesubgenomic promoters. Each non-native subgenomic promoter is capable oftranscribing or expressing adjacent genes or polynucleotide sequences inthe plant host and incapable of recombination with each other and withnative subgenomic promoters. Non-native (foreign) polynucleotidesequences may be inserted adjacent the native plant viral subgenomicpromoter or the native and a non-native plant viral subgenomic promotersif more than one polynucleotide sequence is included. The non-nativepolynucleotide sequences are transcribed or expressed in the host plantunder control of the subgenomic promoter to produce the desiredproducts.

In a second embodiment, a recombinant plant viral polynucleotide isprovided as in the first embodiment except that the native coat proteincoding sequence is placed adjacent one of the non-native coat proteinsubgenomic promoters instead of a non-native coat protein codingsequence.

In a third embodiment, a recombinant plant viral polynucleotide isprovided in which the native coat protein gene is adjacent itssubgenomic promoter and one or more non-native subgenomic promoters havebeen inserted into the viral polynucleotide. The inserted non-nativesubgenomic promoters are capable of transcribing or expressing adjacentgenes in a plant host and are incapable of recombination with each otherand with native subgenomic promoters. Non-native polynucleotidesequences may be inserted adjacent the non-native subgenomic plant viralpromoters such that the sequences are transcribed or expressed in thehost plant under control of the subgenomic promoters to produce thedesired product.

In a fourth embodiment, a recombinant plant viral polynucleotide isprovided as in the third embodiment except that the native coat proteincoding sequence is replaced by a non-native coat protein codingsequence.

The viral vectors are encapsidated by the coat proteins encoded by therecombinant plant viral polynucleotide to produce a recombinant plantvirus. The recombinant plant viral polynucleotide or recombinant plantvirus is used to infect appropriate host plants. The recombinant plantviral polynucleotide is capable of replication in the host, systemicspread in the host, and transcription or expression of foreign gene(s)(exogenous polynucleotide) in the host to produce the desired protein.

Techniques for inoculation of viruses to plants may be found in Fosterand Taylor, eds. “Plant Virology Protocols: From Virus Isolation toTransgenic Resistance (Methods in Molecular Biology (Humana Pr), Vol81)”, Humana Press, 1998; Maramorosh and Koprowski, eds. “Methods inVirology” 7 vols, Academic Press, New York 1967-1984; Hill, S. A.“Methods in Plant Virology”, Blackwell, Oxford, 1984; Walkey, D. G. A.“Applied Plant Virology”, Wiley, New York, 1985; and Kado and Agrawa,eds. “Principles and Techniques in Plant Virology”, VanNostrand-Reinhold, New York.

In addition to the above, the polynucleotide of the present inventioncan also be introduced into a chloroplast genome thereby enablingchloroplast expression.

A technique for introducing exogenous polynucleotide sequences to thegenome of the chloroplasts is known. This technique involves thefollowing procedures. First, plant cells are chemically treated so as toreduce the number of chloroplasts per cell to about one. Then, theexogenous polynucleotide is introduced via particle bombardment into thecells with the aim of introducing at least one exogenous polynucleotidemolecule into the chloroplasts. The exogenous polynucleotides selectedsuch that it is integratable into the chloroplast's genome viahomologous recombination which is readily effected by enzymes inherentto the chloroplast. To this end, the exogenous polynucleotide includes,in addition to a gene of interest, at least one polynucleotide stretchwhich is derived from the chloroplast's genome. In addition, theexogenous polynucleotide includes a selectable marker, which serves bysequential selection procedures to ascertain that all or substantiallyall of the copies of the chloroplast genomes following such selectionwill include the exogenous polynucleotide. Further details relating tothis technique are found in U.S. Pat. Nos. 4,945,050; and 5,693,507which are incorporated herein by reference. A polypeptide can thus beproduced by the protein expression system of the chloroplast and becomeintegrated into the chloroplast's inner membrane.

Since processes which increase yield, seed yield, fiber yield, fiberquality, fiber length, growth rate, biomass, vigor, oil content,fertilizer use efficiency, nitrogen use efficiency and/or abiotic stresstolerance of a plant can involve multiple genes acting additively or insynergy (see, for example, in Quesda et al., Plant Physiol. 130:951-063,2002), the present invention also envisages expressing a plurality ofexogenous polynucleotides in a single host plant to thereby achievesuperior effect on yield, seed yield, fiber yield, fiber quality, fiberlength, growth rate, biomass, vigor, oil content, fertilizer useefficiency, nitrogen use efficiency and/or abiotic stress tolerance of aplant.

Expressing a plurality of exogenous polynucleotides in a single hostplant can be effected by co-introducing multiple nucleic acidconstructs, each including a different exogenous polynucleotide, into asingle plant cell. The transformed cell can than be regenerated into amature plant using the methods described hereinabove.

Alternatively, expressing a plurality of exogenous polynucleotides in asingle host plant can be effected by co-introducing into a singleplant-cell a single nucleic-acid construct including a plurality ofdifferent exogenous polynucleotides. Such a construct can be designedwith a single promoter sequence which can transcribe a polycistronicmessenger RNA including all the different exogenous polynucleotidesequences. To enable co-translation of the different polypeptidesencoded by the polycistronic messenger RNA, the polynucleotide sequencescan be inter-linked via an internal ribosome entry site (IRES) sequencewhich facilitates translation of polynucleotide sequences positioneddownstream of the IRES sequence. In this case, a transcribedpolycistronic RNA molecule encoding the different polypeptides describedabove will be translated from both the capped 5′ end and the twointernal IRES sequences of the polycistronic RNA molecule to therebyproduce in the cell all different polypeptides. Alternatively, theconstruct can include several promoter sequences each linked to adifferent exogenous polynucleotide sequence.

The plant cell transformed with the construct including a plurality ofdifferent exogenous polynucleotides, can be regenerated into a matureplant, using the methods described hereinabove.

Alternatively, expressing a plurality of exogenous polynucleotides in asingle host plant can be effected by introducing different nucleic acidconstructs, including different exogenous polynucleotides, into aplurality of plants. The regenerated transformed plants can then becross-bred and resultant progeny selected for superior abiotic stresstolerance, water use efficiency, fertilizer use efficiency, growth,biomass, yield and/or vigor traits, using conventional plant breedingtechniques.

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder the abiotic stress.

Non-limiting examples of abiotic stress conditions include, salinity,drought, water deprivation, excess of water (e.g., flood, waterlogging),etiolation, low temperature, high temperature, heavy metal toxicity,anaerobiosis, nutrient deficiency, nutrient excess, atmosphericpollution and UV irradiation.

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder fertilizer limiting conditions (e.g., nitrogen-limitingconditions). Non-limiting examples include growing the plant on soilswith low nitrogen content (40-50% Nitrogen of the content present undernormal or optimal conditions), or even under sever nitrogen deficiency(0-10% Nitrogen of the content present under normal or optimalconditions).

Thus, the invention encompasses plants exogenously expressing thepolynucleotide(s), the nucleic acid constructs and/or polypeptide(s) ofthe invention.

Once expressed within the plant cell or the entire plant, the level ofthe polypeptide encoded by the exogenous polynucleotide can bedetermined by methods well known in the art such as, activity assays,Western blots using antibodies capable of specifically binding thepolypeptide, Enzyme-Linked Immuno Sorbent Assay (ELISA),radio-immuno-assays (RIA), immunohistochemistry, immunocytochemistry,immunofluorescence and the like.

Methods of determining the level in the plant of the RNA transcribedfrom the exogenous polynucleotide are well known in the art and include,for example, Northern blot analysis, reverse transcription polymerasechain reaction (RT-PCR) analysis (including quantitative,semi-quantitative or real-time RT-PCR) and RNA-in situ hybridization.

The sequence information and annotations uncovered by the presentteachings can be harnessed in favor of classical breeding. Thus,sub-sequence data of those polynucleotides described above, can be usedas markers for marker assisted selection (MAS), in which a marker isused for indirect selection of a genetic determinant or determinants ofa trait of interest (e.g., biomass, growth rate, oil content, yield,abiotic stress tolerance, water use efficiency, nitrogen use efficiencyand/or fertilizer use efficiency). Nucleic acid data of the presentteachings (DNA or RNA sequence) may contain or be linked to polymorphicsites or genetic markers on the genome such as restriction fragmentlength polymorphism (RFLP), microsatellites and single nucleotidepolymorphism (SNP), DNA fingerprinting (DFP), amplified fragment lengthpolymorphism (AFLP), expression level polymorphism, polymorphism of theencoded polypeptide and any other polymorphism at the DNA or RNAsequence.

Examples of marker assisted selections include, but are not limited to,selection for a morphological trait (e.g., a gene that affects form,coloration, male sterility or resistance such as the presence or absenceof awn, leaf sheath coloration, height, grain color, aroma of rice);selection for a biochemical trait (e.g., a gene that encodes a proteinthat can be extracted and observed; for example, isozymes and storageproteins); selection for a biological trait (e.g., pathogen races orinsect biotypes based on host pathogen or host parasite interaction canbe used as a marker since the genetic constitution of an organism canaffect its susceptibility to pathogens or parasites).

The polynucleotides and polypeptides described hereinabove can be usedin a wide range of economical plants, in a safe and cost effectivemanner.

Plant lines exogenously expressing the polynucleotide or the polypeptideof the invention are screened to identify those that show the greatestincrease of the desired plant trait.

The effect of the transgene (the exogenous polynucleotide encoding thepolypeptide) on abiotic stress tolerance can be determined using knownmethods such as detailed below and in the Examples section whichfollows.

Abiotic stress tolerance—Transformed (i.e., expressing the transgene)and non-transformed (wild type) plants are exposed to an abiotic stresscondition, such as water deprivation, suboptimal temperature (lowtemperature, high temperature), nutrient deficiency, nutrient excess, asalt stress condition, osmotic stress, heavy metal toxicity,anaerobiosis, atmospheric pollution and UV irradiation.

Salinity tolerance assay—Transgenic plants with tolerance to high saltconcentrations are expected to exhibit better germination, seedlingvigor or growth in high salt. Salt stress can be effected in many wayssuch as, for example, by irrigating the plants with a hyperosmoticsolution, by cultivating the plants hydroponically in a hyperosmoticgrowth solution (e.g., Hoagland solution), or by culturing the plants ina hyperosmotic growth medium [e.g., 50% Murashige-Skoog medium (MSmedium)].

Since different plants vary considerably in their tolerance to salinity,the salt concentration in the irrigation water, growth solution, orgrowth medium can be adjusted according to the specific characteristicsof the specific plant cultivar or variety, so as to inflict a mild ormoderate effect on the physiology and/or morphology of the plants (forguidelines as to appropriate concentration see, Bernstein and Kafkafi,Root Growth Under Salinity Stress In: Plant Roots, The Hidden Half 3rded. Waisel Y, Eshel A and Kafkafi U. (editors) Marcel Dekker Inc., NewYork, 2002, and reference therein).

For example, a salinity tolerance test can be performed by irrigatingplants at different developmental stages with increasing concentrationsof sodium chloride (for example 50 mM, 100 mM, 200 mM, 400 mM NaCl)applied from the bottom and from above to ensure even dispersal of salt.Following exposure to the stress condition the plants are frequentlymonitored until substantial physiological and/or morphological effectsappear in wild type plants. Thus, the external phenotypic appearance,degree of wilting and overall success to reach maturity and yieldprogeny are compared between control and transgenic plants.

Quantitative parameters of tolerance measured include, but are notlimited to, the average wet and dry weight, growth rate, leaf size, leafcoverage (overall leaf area), the weight of the seeds yielded, theaverage seed size and the number of seeds produced per plant.Transformed plants not exhibiting substantial physiological and/ormorphological effects, or exhibiting higher biomass than wild-typeplants, are identified as abiotic stress tolerant plants.

Osmotic tolerance test—Osmotic stress assays (including sodium chlorideand mannitol assays) are conducted to determine if an osmotic stressphenotype was sodium chloride-specific or if it was a general osmoticstress related phenotype. Plants which are tolerant to osmotic stressmay have more tolerance to drought and/or freezing. For salt and osmoticstress germination experiments, the medium is supplemented for examplewith 50 mM, 100 mM, 200 mM NaCl or 100 mM, 200 mM NaCl, 400 mM mannitol.

Drought tolerance assay/Osmodcum assay—Tolerance to drought is performedto identify the genes conferring better plant survival after acute waterdeprivation. To analyze whether the transgenic plants are more tolerantto drought, an osmotic stress produced by the non-ionic osmolytesorbitol in the medium can be performed. Control and transgenic plantsare germinated and grown in plant-agar plates for 4 days, after whichthey are transferred to plates containing 500 mM sorbitol. The treatmentcauses growth retardation, then both control and transgenic plants arecompared, by measuring plant weight (wet and dry), yield, and by growthrates measured as time to flowering.

Conversely, soil-based drought screens are performed with plantsoverexpressing the polynucleotides detailed above. Seeds from controlArabidopsis plants, or other transgenic plants overexpressing thepolypeptide of the invention are germinated and transferred to pots.Drought stress is obtained after irrigation is ceased accompanied byplacing the pots on absorbent paper to enhance the soil-drying rate.Transgenic and control plants are compared to each other when themajority of the control plants develop severe wilting. Plants arere-watered after obtaining a significant fraction of the control plantsdisplaying a severe wilting. Plants are ranked comparing to controls foreach of two criteria: tolerance to the drought conditions and recovery(survival) following re-watering.

Cold stress tolerance—To analyze cold stress, mature (25 day old) plantsare transferred to 4° C. chambers for 1 or 2 weeks, with constitutivelight. Later on plants are moved back to greenhouse. Two weeks laterdamages from chilling period, resulting in growth retardation and otherphenotypes, are compared between both control and transgenic plants, bymeasuring plant weight (wet and dry), and by comparing growth ratesmeasured as time to flowering, plant size, yield, and the like. Heatstress tolerance—Heat stress tolerance is achieved by exposing theplants to temperatures above 34° C. for a certain period. Planttolerance is examined after transferring the plants back to 22° C. forrecovery and evaluation after 5 days relative to internal controls(non-transgenic plants) or plants not exposed to neither cold or heatstress.

Water use efficiency—can be determined as the biomass produced per unittranspiration. To analyze WUE, leaf relative water content can bemeasured in control and transgenic plants. Fresh weight (FW) isimmediately recorded; then leaves are soaked for 8 hours in distilledwater at room temperature in the dark, and the turgid weight (TW) isrecorded. Total dry weight (DW) is recorded after drying the leaves at60° C. to a constant weight. Relative water content (RWC) is calculatedaccording to the following Formula I:

RWC=[(FW−DW)/(TW−DW)]×100  Formula I

Fertilizer use efficiency—To analyze whether the transgenic plants aremore responsive to fertilizers, plants are grown in agar plates or potswith a limited amount of fertilizer, as described, for example,Yanagisawa et al (Proc Natl Acad Sci USA. 2004; 101:7833-8). The plantsare analyzed for their overall size, time to flowering, yield, proteincontent of shoot and/or grain. The parameters checked are the overallsize of the mature plant, its wet and dry weight, the weight of theseeds yielded, the average seed size and the number of seeds producedper plant. Other parameters that may be tested are: the chlorophyllcontent of leaves (as nitrogen plant status and the degree of leafverdure is highly correlated), amino acid and the total protein contentof the seeds or other plant parts such as leaves or shoots, oil content,etc. Similarly, instead of providing nitrogen at limiting amounts,phosphate or potassium can be added at increasing concentrations. Again,the same parameters measured are the same as listed above. In this way,nitrogen use efficiency (NUE), phosphate use efficiency (PUE) andpotassium use efficiency (KUE) are assessed, checking the ability of thetransgenic plants to thrive under nutrient restraining conditions.

Nitrogen use efficiency—To analyze whether the transgenic plants (e.g.,Arabidopsis plants) are more responsive to nitrogen, plant are grown in0.75-3 mM (nitrogen deficient conditions) or 6-10 mM (optimal nitrogenconcentration). Plants are allowed to grow for additional 25 days oruntil seed production. The plants are then analyzed for their overallsize, time to flowering, yield, protein content of shoot and/orgrain/seed production. The parameters checked can be the overall size ofthe plant, wet and dry weight, the weight of the seeds yielded, theaverage seed size and the number of seeds produced per plant. Otherparameters that may be tested are: the chlorophyll content of leaves (asnitrogen plant status and the degree of leaf greenness is highlycorrelated), amino acid and the total protein content of the seeds orother plant parts such as leaves or shoots and oil content. Transformedplants not exhibiting substantial physiological and/or morphologicaleffects, or exhibiting higher measured parameters levels than wild-typeplants, are identified as nitrogen use efficient plants.

Nitrogen Use efficiency assay using plantlets—The assay is doneaccording to Yanagisawa-S. et al. with minor modifications (“Metabolicengineering with Dof1 transcription factor in plants: Improved nitrogenassimilation and growth under low-nitrogen conditions” Proc. Natl. Acad.Sci. USA 101, 7833-7838). Briefly, transgenic plants which are grown for7-10 days in 0.5×MS [Murashige-Skoog] supplemented with a selectionagent are transferred to two nitrogen-limiting conditions: MS media inwhich the combined nitrogen concentration (NH₄NO₃ and KNO₃) was 0.75 mM(nitrogen deficient conditions) or 6-15 mM (optimal nitrogenconcentration). Plants are allowed to grow for additional 30-40 days andthen photographed, individually removed from the Agar (the shoot withoutthe roots) and immediately weighed (fresh weight) for later statisticalanalysis. Constructs for which only T1 seeds are available are sown onselective media and at least 20 seedlings (each one representing anindependent transformation event) are carefully transferred to thenitrogen-limiting media. For constructs for which T2 seeds areavailable, different transformation events are analyzed. Usually, 20randomly selected plants from each event are transferred to thenitrogen-limiting media allowed to grow for 3-4 additional weeks andindividually weighed at the end of that period. Transgenic plants arecompared to control plants grown in parallel under the same conditions.Mock-transgenic plants expressing the uidA reporter gene (GUS) under thesame promoter or transgenic plants carrying the same promoter butlacking a reporter gene are used as control.

Nitrogen determination—The procedure for N (nitrogen) concentrationdetermination in the structural parts of the plants involves thepotassium persulfate digestion method to convert organic N to NO₃ ⁻(Purcell and King 1996 Argon. J. 88:111-113, the modified Cd⁻ mediatedreduction of NO₃ ⁻ to NO₂ ⁻ (Vodovotz 1996 Biotechniques 20:390-394) andthe measurement of nitrite by the Griess assay (Vodovotz 1996, supra).The absorbance values are measured at 550 nm against a standard curve ofNaNO₂. The procedure is described in details in Samonte et al. 2006Agron. J. 98:168-176.

Germination tests—Germination tests compare the percentage of seeds fromtransgenic plants that could complete the germination process to thepercentage of seeds from control plants that are treated in the samemanner. Normal conditions are considered for example, incubations at 22°C. under 22-hour light 2-hour dark daily cycles. Evaluation ofgermination and seedling vigor is conducted between 4 and 14 days afterplanting. The basal media is 50% MS medium (Murashige and Skoog, 1962Plant Physiology 15, 473-497).

Germination is checked also at unfavorable conditions such as cold(incubating at temperatures lower than 10° C. instead of 22° C.) orusing seed inhibition solutions that contain high concentrations of anosmolyte such as sorbitol (at concentrations of 50 mM, 100 mM, 200 mM,300 mM, 500 mM, and up to 1000 mM) or applying increasing concentrationsof salt (of 50 mM, 100 mM, 200 mM, 300 mM, 500 mM NaCl).

The effect of the transgene on plant's vigor, growth rate, biomass,yield and/or oil content can be determined using known methods.

Plant vigor—The plant vigor can be calculated by the increase in growthparameters such as leaf area, fiber length, rosette diameter, plantfresh weight and the like per time.

Growth rate—The growth rate can be measured using digital analysis ofgrowing plants. For example, images of plants growing in greenhouse onplot basis can be captured every 3 days and the rosette area can becalculated by digital analysis. Rosette area growth is calculated usingthe difference of rosette area between days of sampling divided by thedifference in days between samples.

Evaluation of growth rate can be done by measuring plant biomassproduced, rosette area, leaf size or root length per time (can bemeasured in cm² per day of leaf area).

Relative growth area can be calculated using Formula II.

Relative growth rate area=Regression coefficient of area along timecourse  Formula II

-   -   Thus, the relative growth area rate is in units of 1/day and        length growth rate is in units of 1/day.

Seed yield—Evaluation of the seed yield per plant can be done bymeasuring the amount (weight or size) or quantity (i.e., number) of dryseeds produced and harvested from 8-16 plants and divided by the numberof plants.

For example, the total seeds from 8-16 plants can be collected, weightedusing e.g., an analytical balance and the total weight can be divided bythe number of plants. Seed yield per growing area can be calculated inthe same manner while taking into account the growing area given to asingle plant. Increase seed yield per growing area could be achieved byincreasing seed yield per plant, and/or by increasing number of plantscapable of growing in a given area.

In addition, seed yield can be determined via the weight of 1000 seeds.The weight of 1000 seeds can be determined as follows: seeds arescattered on a glass tray and a picture is taken. Each sample isweighted and then using the digital analysis, the number of seeds ineach sample is calculated.

The 1000 seeds weight can be calculated using formula III:

1000 Seed Weight=number of seed in sample/sample weight×1000  FormulaIII

The Harvest Index can be calculated using Formula IV

Harvest Index=Average seed yield per plant/Average dry weight  FormulaIV

Grain protein concentration—Grain protein content (g grain protein m⁻²)is estimated as the product of the mass of grain N (g grain N m⁻²)multiplied by the N/protein conversion ratio of k-5.13 (Mosse 1990,supra). The grain protein concentration is estimated as the ratio ofgrain protein content per unit mass of the grain (g grain protein kg⁻¹grain).

Fiber length—Fiber length can be measured using fibrograph. Thefibrograph system was used to compute length in terms of “Upper HalfMean” length. The upper half mean (UHM) is the average length of longerhalf of the fiber distribution. The fibrograph measures length in spanlengths at a given percentage point (Hypertext Transfer Protocol://WorldWide Web (dot) cottoninc (dot) com/ClassificationofCotton/?Pg=4#Length).

According to some embodiments of the invention, increased yield of cornmay be manifested as one or more of the following: increase in thenumber of plants per growing area, increase in the number of ears perplant, increase in the number of rows per ear, number of kernels per earrow, kernel weight, thousand kernel weight (1000-weight), earlength/diameter, increase oil content per kernel and increase starchcontent per kernel.

As mentioned, the increase of plant yield can be determined by variousparameters. For example, increased yield of rice may be manifested by anincrease in one or more of the following: number of plants per growingarea, number of panicles per plant, number of spikelets per panicle,number of flowers per panicle, increase in the seed filling rate,increase in thousand kernel weight (1000-weight), increase oil contentper seed, increase starch content per seed, among others. An increase inyield may also result in modified architecture, or may occur because ofmodified architecture.

Similarly, increased yield of soybean may be manifested by an increasein one or more of the following: number of plants per growing area,number of pods per plant, number of seeds per pod, increase in the seedfilling rate, increase in thousand seed weight (1000-weight), reduce podshattering, increase oil content per seed, increase protein content perseed, among others. An increase in yield may also result in modifiedarchitecture, or may occur because of modified architecture.

Increased yield of canola may be manifested by an increase in one ormore of the following: number of plants per growing area, number of podsper plant, number of seeds per pod, increase in the seed filling rate,increase in thousand seed weight (1000-weight), reduce pod shattering,increase oil content per seed, among others. An increase in yield mayalso result in modified architecture, or may occur because of modifiedarchitecture.

Increased yield of cotton may be manifested by an increase in one ormore of the following: number of plants per growing area, number ofbolls per plant, number of seeds per boll, increase in the seed fillingrate, increase in thousand seed weight (1000-weight), increase oilcontent per seed, improve fiber length, fiber strength, among others. Anincrease in yield may also result in modified architecture, or may occurbecause of modified architecture.

Oil content—The oil content of a plant can be determined by extractionof the oil from the seed or the vegetative portion of the plant.Briefly, lipids (oil) can be removed from the plant (e.g., seed) bygrinding the plant tissue in the presence of specific solvents (e.g.,hexane or petroleum ether) and extracting the oil in a continuousextractor. Indirect oil content analysis can be carried out usingvarious known methods such as Nuclear Magnetic Resonance (NMR)Spectroscopy, which measures the resonance energy absorbed by hydrogenatoms in the liquid state of the sample [See for example, Conway T F.and Earle F R., 1%3, Journal of the American Oil Chemists' Society;Springer Berlin/Heidelberg, ISSN: 0003-021X (Print) 1558-9331 (Online)];the Near Infrared (NI) Spectroscopy, which utilizes the absorption ofnear infrared energy (1100-2500 nm) by the sample; and a methoddescribed in WO/2001/023884, which is based on extracting oil a solvent,evaporating the solvent in a gas stream which forms oil particles, anddirecting a light into the gas stream and oil particles which forms adetectable reflected light.

Thus, the present invention is of high agricultural value for promotingthe yield of commercially desired crops (e.g., biomass of vegetativeorgan such as poplar wood, or reproductive organ such as number of seedsor seed biomass).

Any of the transgenic plants described hereinabove or parts thereof maybe processed to produce a feed, meal, protein or oil preparation, suchas for ruminant animals.

The transgenic plants described hereinabove, which exhibit an increasedoil content can be used to produce plant oil (by extracting the oil fromthe plant).

The plant oil (including the seed oil and/or the vegetative portion oil)produced according to the method of the invention may be combined with avariety of other ingredients. The specific ingredients included in aproduct are determined according to the intended use. Exemplary productsinclude animal feed, raw material for chemical modification,biodegradable plastic, blended food product, edible oil, biofuel,cooking oil, lubricant, biodiesel, snack food, cosmetics, andfermentation process raw material. Exemplary products to be incorporatedto the plant oil include animal feeds, human food products such asextruded snack foods, breads, as a food binding agent, aquaculturefeeds, fermentable mixtures, food supplements, sport drinks, nutritionalfood bars, multi-vitamin supplements, diet drinks, and cereal foods.

According to some embodiments of the invention, the oil comprises a seedoil.

According to some embodiments of the invention, the oil comprises avegetative portion oil (oil of the vegetative portion of the plant).

According to some embodiments of the invention, the plant cell forms apart of a plant.

As used herein the term “about” refers to ±10%.

The terms “comprises”, “comprising”, “includes”, “including”, “having”and their conjugates mean “including but not limited to”.

The term “consisting of” means “including and limited to”.

The term “consisting essentially of” means that the composition, methodor structure may include additional ingredients, steps and/or parts, butonly if the additional ingredients, steps and/or parts do not materiallyalter the basic and novel characteristics of the claimed composition,method or structure.

As used herein, the singular form “a”, “an” and “the” include pluralreferences unless the context clearly dictates otherwise. For example,the term “a compound” or “at least one compound” may include a pluralityof compounds, including mixtures thereof.

Throughout this application, various embodiments of this invention maybe presented in a range format. It should be understood that thedescription in range format is merely for convenience and brevity andshould not be construed as an inflexible limitation on the scope of theinvention. Accordingly, the description of a range should be consideredto have specifically disclosed all the possible subranges as well asindividual numerical values within that range. For example, descriptionof a range such as from 1 to 6 should be considered to have specificallydisclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numberswithin that range, for example, 1, 2, 3, 4, 5, and 6. This appliesregardless of the breadth of the range.

Whenever a numerical range is indicated herein, it is meant to includeany cited numeral (fractional or integral) within the indicated range.The phrases “ranging/ranges between” a first indicate number and asecond indicate number and “ranging/ranges from” a first indicate number“to” a second indicate number are used herein interchangeably and aremeant to include the first and second indicated numbers and all thefractional and integral numerals therebetween.

As used herein the term “method” refers to manners, means, techniquesand procedures for accomplishing a given task including, but not limitedto, those manners, means, techniques and procedures either known to, orreadily developed from known manners, means, techniques and proceduresby practitioners of the chemical, pharmacological, biological,biochemical and medical arts.

It is appreciated that certain features of the invention, which are, forclarity, described in the context of separate embodiments, may also beprovided in combination in a single embodiment. Conversely, variousfeatures of the invention, which are, for brevity, described in thecontext of a single embodiment, may also be provided separately or inany suitable subcombination or as suitable in any other describedembodiment of the invention. Certain features described in the contextof various embodiments are not to be considered essential features ofthose embodiments, unless the embodiment is inoperative without thoseelements.

Various embodiments and aspects of the present invention as delineatedhereinabove and as claimed in the claims section below find experimentalsupport in the following examples.

EXAMPLES

Reference is now made to the following examples, which together with theabove descriptions illustrate some embodiments of the invention in a nonlimiting fashion.

Generally, the nomenclature used herein and the laboratory proceduresutilized in the present invention include molecular, biochemical,microbiological and recombinant DNA techniques. Such techniques arethoroughly explained in the literature. See, for example, “MolecularCloning: A laboratory Manual” Sambrook et al., (1989); “CurrentProtocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed.(1994); Ausubel et al., “Current Protocols in Molecular Biology”, JohnWiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide toMolecular Cloning”, John Wiley & Sons, New York (1988); Watson et al.,“Recombinant DNA”, Scientific American Books, New York; Birren et al.(eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, ColdSpring Harbor Laboratory Press, New York (1998); methodologies as setforth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis,J. E., ed. (1994); “Current Protocols in Immunology” Volumes I-IllColigan J. E., ed. (1994); Stites et al. (eds), “Basic and ClinicalImmunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994);Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W.H. Freeman and Co., New York (1980); available immunoassays areextensively described in the patent and scientific literature, see, forexample, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578;3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533;3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521;“Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic AcidHybridization” Hames, B. D., and Higgins S. J., eds. (1985);“Transcription and Translation” Hames, B. D., and Higgins S. J., Eds.(1984); “Animal Cell Culture” Freshney, R. I., ed. (1986); “ImmobilizedCells and Enzymes” IRL Press, (1986); “A Practical Guide to MolecularCloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317,Academic Press; “PCR Protocols: A Guide To Methods And Applications”,Academic Press, San Diego, Calif. (1990); Marshak et al., “Strategiesfor Protein Purification and Characterization—A Laboratory CourseManual” CSHL Press (1996); all of which are incorporated by reference asif fully set forth herein. Other general references are providedthroughout this document. The procedures therein are believed to be wellknown in the art and are provided for the convenience of the reader. Allthe information contained therein is incorporated herein by reference.

General Experimental and Bioinformatics Methods

RNA extraction—Tissues growing at various growth conditions (asdescribed below) were sampled and RNA was extracted using TRIzol Reagentfrom Invitrogen [Hypertext Transfer Protocol://World Wide Web (dot)invitrogen (dot) con/content (dot)cfm?pageid=469]. Approximately 30-50mg of tissue was taken from samples. The weighed tissues were groundusing pestle and mortar in liquid nitrogen and resuspended in 500 μl ofTRIzol Reagent. To the homogenized lysate, 100 μl of chloroform wasadded followed by precipitation using isopropanol and two washes with75% ethanol. The RNA was eluted in 30 μl of RNase-free water. RNAsamples were cleaned up using Qiagen's RNeasy minikit clean-up protocolas per the manufacturer's protocol (QIAGEN Inc, CA USA). Forconvenience, each micro-array expression information tissue type hasreceived an expression Set ID.

Correlation analysis—was performed for selected genes according to someembodiments of the invention, in which the characterized parameters(measured parameters according to the correlation IDs) were used as “xaxis” for correlation with the tissue transcriptom which was used as the“Y axis”. For each gene and measured parameter a correlation coefficient“R” was calculated [using Pearson correlation test Hypertext TransferProtocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739(dot) html] along with a p-value for the significance of thecorrelation. When the correlation coefficient (R) between the levels ofa gene's expression in a certain tissue and a phenotypic performanceacross ecotypes/variety/hybrid is high in absolute value (between0.5-1), there is an association between the gene (specifically theexpression level of this gene) the phenotypic characteristic (e.g.,improved nitrogen use efficiency, abiotic stress tolerance, yield,growth rate and the like). A positive correlation indicates that theexpression of the gene in a certain tissue or developmental stage andthe correlation vector (phenotype performance) are positively associated(both, expression and phenotypic performance increase or decreasesimultaneously) while a negative correlation indicates a negativeassociation (while the one is increasing the other is decreasing andvice versa).

Example 1 Identification of Genes and Predicted Role UsingBioinformatics Tools

The present inventors have identified polynucleotides which can increaseplant yield, seed yield, oil yield, oil content, biomass, growth rate,fiber yield and/or quality, abiotic stress tolerance, nitrogen useefficiency and/or vigor of a plant, as follows.

The nucleotide sequence datasets used here were from publicly availabledatabases or from sequences obtained using the Solexa technology (e.g.Barley and Sorghum). Sequence data from 100 different plant species wasintroduced into a single, comprehensive database. Other information ongene expression, protein annotation, enzymes and pathways were alsoincorporated. Major databases used include:

Genomes

Arabidopsis genome [TAIR genome version 8 (Hypertext TransferProtocol://World Wide Web (dot) arabidopsis (dot) org/)];

Rice genome [build 6.0 (Hypertext Transfer Protocol://rice (dot)plantbiology(dot)msu(dot)edu/index.shtml];

Poplar [Populus trichocarpa release 1.1 from JGI (assembly release v1.0)(Hypertext Transfer Protocol://World Wide Web (dot) genome (dot) jgi-psf(dot) org/)];

Brachypodium [JGI 4× assembly, Hypertext Transfer Protocol://World WideWeb (dot) brachpodium (dot) org)];

Soybean [DOE-JGI SCP, version Glymal (Hypertext TransferProtocol://World Wide Web (dot) phytozome (dot) net/)];

Grape [French-Italian Public Consortium for Grapevine GenomeCharacterization grapevine genome (Hypertext Transfer Protocol://WorldWide Web (dot) genoscope (dot) cns (dot) fr)];

Castobean [TIGR/J Craig Venter Institute 4× assembly [(HypertextTransfer Protocol://msc (dot) jcvi (dot) org/r communis];

Sorghum [DOE-JGI SCP, version Sbi1 [Hypertext Transfer Protocol://WorldWide Web (dot) phytozome (dot) net/)];

Partially assembled genome of Maize [Hypertext TransferProtocol://maizesequence (dot) org/];

Expressed EST and mRNA sequences were extracted from the followingdatabases:

EST and RNA sequences from NCBI (Hypertext Transfer Protocol://WorldWide Web (dot) ncbi (dot) nlm (dot) nih (dot) gov/dbEST/);

RefSeq (Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot)nlm (dot) nih (dot) gov/RefSeq/);

TAIR (Hypertext Transfer Protocol://World Wide Web (dot) arabidopsis(dot) org/);

Protein and Pathway Databases

Uniprot [Hypertext Transfer Protocol://World Wide Web (dot) uniprot(dot) org/].

AraCyc [Hypertext Transfer Protocol://World Wide Web (dot) arabidopsis(dot) org/biocyc/index (dot) jsp].

ENZYME [Hypertext Transfer Protocol://expasy (dot) org/enzyme/].

Microarray datasets were downloaded from:

GEO (Hypertext Transfer Protocol://World Wide Web.ncbi.nlm.nih.gov/geo/)TAIR (Hypertext Transfer Protocol://World Wide Web.arabidopsis.org/).

Proprietary microarray data (See WO2008/122980) and Examples 2-9 below.

QTL and SNPs Information

Gramene [Hypertext Transfer Protocol://World Wide Web (dot) gramene(dot) org/qtl/].

Panzea [Hypertext Transfer Protocol://World Wide Web (dot) panzea (dot)org/index (dot) html].

Database Assembly—was performed to build a wide, rich, reliableannotated and easy to analyze database comprised of publicly availablegenomic mRNA, ESTs DNA sequences, data from various crops as well asgene expression, protein annotation and pathway data QTLs, and otherrelevant information.

Database assembly is comprised of a toolbox of gene refining,structuring, annotation and analysis tools enabling to construct atailored database for each gene discovery project. Gene refining andstructuring tools enable to reliably detect splice variants andantisense transcripts, generating understanding of various potentialphenotypic outcomes of a single gene. The capabilities of the “LEADS”platform of Compugen LTD for analyzing human genome have been confirmedand accepted by the scientific community [see e.g., “WidespreadAntisense Transcription”, Yelin, et al. (2003) Nature Biotechnology 21,379-85; “Splicing of Alu Sequences”, Lev-Maor, et al. (2003) Science 300(5623), 1288-91; “Computational analysis of alternative splicing usingEST tissue information”, Xie H et al. Genomics 2002], and have beenproven most efficient in plant genomics as well.

EST clustering and gene assembly—For gene clustering and assembly oforganisms with available genome sequence data (arabidopsis, rice,castorbean, grape, brachypodium, poplar, soybean, sorghum) the genomicLEADS version (GANG) was employed. This tool allows most accurateclustering of ESTs and mRNA sequences on genome, and predicts genestructure as well as alternative splicing events and anti-sensetranscription.

For organisms with no available full genome sequence data, “expressedLEADS” clustering software was applied.

Gene annotation—Predicted genes and proteins were annotated as follows:

BLAST® search [Hypertext Transfer Protocol://blast(dot)ncbi(dot)nlm(dot)nih(dot)gov/Blast(dot)cgi] against all plant UniProt [Hypertext TransferProtocol://World Wide Web(dot)uniprot(dot)org/] sequences was performed.Open reading frames of each putative transcript were analyzed andlongest ORF with higher number of homologues was selected as predictedprotein of the transcript. The predicted proteins were analyzed byInterPro [Hypertext Transfer Protocol://World WideWeb(dot)ebi(dot)ac(dot)uk/interpro/].

BLAST® against proteins from AraCyc and ENZYME databases was used to mapthe predicted transcripts to AraCyc pathways.

Predicted proteins from different species were compared using BLAST®algorithm [Hypertext Transfer Protocol://World WideWeb(dot)ncbi(dot)nlm(dot)nih (dot)gov/Blast(dot)cgi] to validate theaccuracy of the predicted protein sequence, and for efficient detectionof orthologs.

Gene expression profiling—Several data sources were exploited for geneexpression profiling which combined microarray data and digitalexpression profile (see below). According to gene expression profile, acorrelation analysis was performed to identify genes which areco-regulated under different developmental stages and environmentalconditions and which are associated with different phenotypes.

Publicly available microarray datasets were downloaded from TAIR andNCBI GEO sites, renormalized, and integrated into the database.Expression profiling is one of the most important resource data foridentifying genes important for yield, biomass, growth rate, vigor, oilcontent, abiotic stress tolerance of plants and nitrogen use efficiency.

A digital expression profile summary was compiled for each clusteraccording to all keywords included in the sequence records comprisingthe cluster. Digital expression, also known as electronic Northern Blot,is a tool that displays virtual expression profile based on the ESTsequences forming the gene cluster. The tool provides the expressionprofile of a cluster in terms of plant anatomy (e.g., the tissue/organin which the gene is expressed), developmental stage (e.g., thedevelopmental stages at which a gene can be found/expressed) and profileof treatment (provides the physiological conditions under which a geneis expressed such as drought, cold, pathogen infection, etc). Given arandom distribution of ESTs in the different clusters, the digitalexpression provides a probability value that describes the probabilityof a cluster having a total of N ESTs to contain X ESTs from a certaincollection of libraries. For the probability calculations, the followingis taken into consideration: a) the number of ESTs in the cluster, b)the number of ESTs of the implicated and related libraries, c) theoverall number of ESTs available representing the species. Therebyclusters with low probability values are highly enriched with ESTs fromthe group of libraries of interest indicating a specialized expression.

Recently, the accuracy of this system was demonstrated by Portnoy etal., 2009 (Analysis Of The Melon Fruit Transcriptome Based On 454Pyrosequencing) in: Plant & Animal Genomes XVH Conference, San Diego,Calif. Transcriptomic analysis, based on relative EST abundance in datawas performed by 454 pyrosequencing of cDNA representing mRNA of themelon fruit. Fourteen double strand cDNA samples obtained from twogenotypes, two fruit tissues (flesh and rind) and four developmentalstages were sequenced. GS FLX pyrosequencing (Roche/454 Life Sciences)of non-normalized and purified cDNA samples yielded 1,150,657 expressedsequence tags that assembled into 67,477 unigenes (32,357 singletons and35,120 contigs). Analysis of the data obtained against the CucurbitGenomics Database [Hypertext Transfer Protocol://World Wide Web (dot)icugi (dot) org/] confirmed the accuracy of the sequencing and assembly.Expression patterns of selected genes fitted well their qRT-PCR data.

Example 2 Production of Arabidopsis Transcriptom and High ThroughputCorrelation Analysis of Yield, Biomass and/or Vigor Related ParametersUsing 44K Arabidopsis Full Genome Oligonucleotide Micro-Array

To produce a high throughput correlation analysis, the present inventorsutilized an Arabidopsis thaliana oligonucleotide micro-array, producedby Agilent Technologies [Hypertext Transfer Protocol://World Wide Web(dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879].The array oligonucleotide represents about 40,000 A. thaliana genes andtranscripts designed based on data from the TIGR ATH1 v.5 database andArabidopsis MPSS (University of Delaware) databases. To definecorrelations between the levels of RNA expression and yield, biomasscomponents or vigor related parameters, various plant characteristics of15 different Arabidopsis ecotypes were analyzed. Among them, nineecotypes encompassing the observed variance were selected for RNAexpression analysis. The correlation between the RNA levels and thecharacterized parameters was analyzed using Pearson correlation test[Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot)com/hyperstat/A34739 (dot) html].

Experimental Procedures

Analyzed Arabidopsis tissues—Five tissues at different developmentalstages including root, leaf, flower at anthesis, seed at 5 days afterflowering (DAF) and seed at 12 DAF, representing different plantcharacteristics, were sampled and RNA was extracted as described asdescribed hereinabove under “GENERAL EXPERIMENTAL AND BIOINFORMATICSMETHODS”. For convenience, each micro-array expression informationtissue type has received a Set ID as summarized in Table 1 below.

TABLE 1 Tissues used for Arabidopsis transcriptom expression setsExpression Set Set ID Root at reproductive stage 1 Seed 5 DAF atreproductive stage 2 Seed 12 DAF at reproductive stage 3 Flower atreproductive stage 4 Leaf at reproductive stage 5 Provided are theidentification (ID) digits of each of the Arabidopsis expression sets(1-5). DAF = days after flowering.

Yield components and vigor related parameters assessment—Eight out ofthe nine Arabidopsis ecotypes were used in each of 5 repetitive blocks(named A, B, C, D and E), each containing 20 plants per plot. The plantswere grown in a greenhouse at controlled conditions in 22° C., and theN:P:K fertilizer (20:20:20; weight ratios) [nitrogen (N), phosphorus (P)and potassium (K)] was added. During this time data was collected,documented and analyzed. Additional data was collected through theseedling stage of plants grown in a tissue culture in vertical growntransparent agar plates. Most of chosen parameters were analyzed bydigital imaging.

Digital imaging in Tissue culture—A laboratory image acquisition systemwas used for capturing images of plantlets sawn in square agar plates.The image acquisition system consists of a digital reflex camera (CanonEOS 300D) attached to a 55 mm focal length lens (Canon EF-S series),mounted on a reproduction device (Kaiser RS), which included 4 lightunits (4×150 Watts light bulb) and located in a darkroom.

Digital imaging in Greenhouse—The image capturing process was repeatedevery 3-4 days starting at day 7 till day 30. The same camera attachedto a 24 mm focal length lens (Canon EF series), placed in a custom madeiron mount, was used for capturing images of larger plants sawn in whitetubs in an environmental controlled greenhouse. The white tubs weresquare shape with measurements of 36×26.2 cm and 7.5 cm deep. During thecapture process, the tubs were placed beneath the iron mount, whileavoiding direct sun light and casting of shadows. This process wasrepeated every 3-4 days for up to 30 days.

An image analysis system was used, which consists of a personal desktopcomputer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ1.37, Java based image processing program, which was developed at theU.S National Institutes of Health and is freely available on theinternet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/.Images were captured in resolution of 6 Mega Pixels (3072×2048 pixels)and stored in a low compression JPEG (Joint Photographic Experts Groupstandard) format. Next, analyzed data was saved to text files andprocessed using the JMP statistical analysis software (SAS institute).

Leaf analysis—Using the digital analysis leaves data was calculated,including leaf number, area, perimeter, length and width. On day 30, 3-4representative plants were chosen from each plot of blocks A, B and C.The plants were dissected, each leaf was separated and was introducedbetween two glass trays, a photo of each plant was taken and the variousparameters (such as leaf total area, laminar length etc.) werecalculated from the images. The blade circularity was calculated aslaminar width divided by laminar length.

Root analysis—During 17 days, the different ecotypes were grown intransparent agar plates. The plates were photographed every 3 daysstarting at day 7 in the photography room and the roots development wasdocumented (see examples in FIGS. 3A-3F). The growth rate of roots wascalculated according to Formula V.

Relative growth rate of root coverage=Regression coefficient of rootcoverage along time course.  Formula V

Vegetative growth rate analysis—was calculated according to Formula VI.The analysis was ended with the appearance of overlapping plants.

Relative vegetative growth rate area=Regression coefficient ofvegetative area along time course.  Formula VI

For comparison between ecotypes the calculated rate was normalized usingplant developmental stage as represented by the number of true leaves.In cases where plants with 8 leaves had been sampled twice (for exampleat day 10 and day 13), only the largest sample was chosen and added tothe Anova comparison.

Seeds in siliques analysis—On day 70, 15-17 siliques were collected fromeach plot in blocks D and E. The chosen siliques were light brown colorbut still intact. The siliques were opened in the photography room andthe seeds were scatter on a glass tray, a high resolution digitalpicture was taken for each plot. Using the images the number of seedsper silique was determined.

Seeds average weight—At the end of the experiment all seeds from plotsof blocks A-C were collected. An average weight of 0.02 grams wasmeasured from each sample, the seeds were scattered on a glass tray anda picture was taken. Using the digital analysis, the number of seeds ineach sample was calculated.

Oil percentage in seeds—At the end of the experiment all seeds fromplots of blocks A-C were collected. Columbia seeds from 3 plots weremixed grounded and then mounted onto the extraction chamber. 210 ml ofn-Hexane (Cat No. 080951 Biolab Ltd.) were used as the solvent. Theextraction was performed for 30 hours at medium heat 50° C. Once theextraction has ended the n-Hexane was evaporated using the evaporator at35° C. and vacuum conditions. The process was repeated twice. Theinformation gained from the Soxhlet extractor (Soxhlet, F. Diegewichtsanalytische Bestimmung des Milchfettes, Polytechnisches J.(Dingler's) 1879, 232, 461) was used to create a calibration curve forthe Low Resonance NMR. The content of oil of all seed samples wasdetermined using the Low Resonance NMR (MARAN Ultra-Oxford Instrument)and its MultiQuant sowftware package.

Silique length analysis—On day 50 from sowing, 30 siliques fromdifferent plants in each plot were sampled in block A. The chosensiliques were green-yellow in color and were collected from the bottomparts of a grown plant's stem. A digital photograph was taken todetermine silique's length.

Dry weight and seed yield—On day 80 from sowing, the plants from blocksA-C were harvested and left to dry at 30° C. in a drying chamber. Thebiomass and seed weight of each plot was separated, measured and dividedby the number of plants. Dry weight=total weight of the vegetativeportion above ground (excluding roots) after drying at 30° C. in adrying chamber; Seed yield per plant=total seed weight per plant (gr).

Oil yield—The oil yield was calculated using Formula VII.

Seed Oil yield=Seed yield per plant (gr.)*Oil % in seed.  Formula VII

Harvest Index (seed)—The harvest index was calculated using Formula IV(described above): Harvest Index=Average seed yield per plant/Averagedry weight.

Experimental Results

Nine different Arabidopsis ecotypes were grown and characterized for 18parameters (named as vectors).

TABLE 2 Arabidopsis correlated parameters (vectors) Correlated parameterwith Correlation ID Seeds per silique (number) 1 Harvest Index (value) 2seed yield per plant (gr) 3 Dry matter per plant (gr) 4 Total Leaf Areaper plant (cm) 5 Oil % per seed (percent) 6 Oil yield per plant (mg) 7relative root growth (cm/day) 8 root length day 7 (cm) 9 root length day13 (cm) 10 fresh weight (gr) 11 seed weight (gr) 12 Vegetative growthrate (cm²/day) 13 Lamina length (cm) 14 Lamina width(cm) 15 Leafwidth/length (ratio) 16 Blade circularity (cm) 17 Silique length (cm) 18Provided are the Arabidopsis correlated parameters (correlation ID Nos.1-18). Abbreviations: Cm = centimeter(s); gr = gram(s); mg =milligram(s).

The characterized values are summarized in Table 3 and 4 below and thecorrelation analysis is provided in Table 5 below.

TABLE 3 Measured parameters in Arabidopsis ecotypes Ecotype/CorrelationID No. Line-1 Line-2 Line-3 Line-4 Line-5 1 45.44 53.47 58.47 35.2748.56 2 0.53 0.35 0.56 0.33 0.37 3 0.34 0.44 0.59 0.42 0.61 4 0.64 1.271.05 1.28 1.69 5 46.86 109.89 58.36 56.8 114.66 6 34.42 31.19 38.0527.76 35.49 7 118.63 138.73 224.06 116.26 218.27 8 0.631 0.664 1.1761.089 0.907 9 0.937 1.759 0.701 0.728 0.991 10 4.419 8.53 5.621 4.8345.957 11 1.51 3.607 1.935 2.082 3.556 12 0.02031238 0.023022440.02522553 0.03/14/1936 0.02021001 13 0.31258158 0.37755231 0.48412540.47415969 0.42508143 14 2.76683 3.54357 3.27353 3.78465 3.68982 151.38477 1.69708 1.45982 1.37418 1.82816 16 0.352785 0.287757 0.3159930.258499 0.356279 17 0.508828 0.48083 0.45029 0.369857 0.500566 18 1.061.26 1.31 1.47 1.24 Provided are the values of each of the parametersmeasured in Arabidopsis ecotypes (lines 1-5) using the correlation IDnumbers described in Table 2 hereinabove.

TABLE 4 Measured parameters in Arabidopsis ecotypes-continueEcotype/Correlation ID No. Line-6 Line-7 Line-8 Line-9 1 37 39.38 40.5325.53 2 0.32 0.45 0.51 0.41 3 0.43 0.36 0.62 0.55 4 1.34 0.81 1.21 1.355 110.82 88.49 121.79 93.04 6 32.91 31.56 30.79 34.02 7 142.11 114.15190.06 187.62 8 0.774 0.606 0.701 0.782 9 1.163 1.284 1.414 1.251 106.372 5.649 7.06 7.041 11 4.338 3.467 3.479 3.71 12 0.026343530.02048623 0.02260485 0.02352516 13 0.64454891 0.42961167 0.384237820.47130278 14 4.59654 3.87735 3.71722 4.14899 15 1.64999 1.51005 1.816911.66772 16 0.272645 0.304707 0.335145 0.306598 17 0.375805 0.3937450.491283 0.408787 18 1.09 1.18 1.18 1 Provided are the values of each ofthe parameters measured in Arabidopsis ecotypes (lines 6-9) using thecorrelation ID numbers described in Table 2 hereinabove.

TABLE 5 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across Arabidopsis accessions GeneExp. Corr. R Exp. Corr. Name R P value set ID Name Gene P value set IDLYD289 0.92 3.17E−03 2 18 LYD289 0.90 2.54E−03 4 18 LYD289 0.75 3.34E−025 3 LYD289 0.75 3.25E−02 5 7 LYD290 0.77 2.42E−02 1 18 LYD290 0.793.33E−02 2 9 LYD290 0.71 4.87E−02 3 2 LYD291 0.89 7.19E−03 2 2 LYD2910.76 4.58E−02 2 6 LYD291 0.71 4.76E−02 3 18 LYD292 0.70 5.11E−02 1 1LYD292 0.73 4.16E−02 4 8 LYD292 0.74 3.48E−02 5 12 LYD292 0.81 1.44E−025 18 LYD293 0.71 4.72E−02 3 18 LYD293 0.72 4.28E−02 5 3 LYD293 0.743.65E−02 5 7 LYD293 0.76 3.03E−02 5 8 LYD294 0.74 3.55E−02 1 18 LYD2940.81 1.57E−02 5 12 LYD294 0.79 2.01E−02 5 18 LYD295 0.73 3.83E−02 1 18LYD295 0.80 3.03E−02 2 2 LYD295 0.79 2.08E−02 3 3 LYD295 0.71 4.92E−02 37 LYD295 0.72 4.32E−02 5 1 LYD296 0.76 4.69E−02 2 18 LYD296 0.764.57E−02 2 3 LYD296 0.77 4.34E−02 2 7 LYD296 0.86 5.77E−03 3 18 LYD2970.86 1.23E−02 2 1 LYD297 0.76 4.69E−02 2 18 LYD297 0.84 8.28E−03 3 4LYD297 0.76 3.03E−02 5 12 LYD297 0.75 3.32E−02 5 18 LYD298 0.70 7.71E−022 1 LYD298 0.72 6.93E−02 2 18 LYD298 0.88 3.55E−03 3 12 LYD298 0.753.28E−02 3 18 LYD299 0.85 7.67E−03 1 12 LYD299 0.76 2.79E−02 1 18 LYD2990.71 7.32E−02 2 14 LYD299 0.87 1.19E−02 2 13 LYD299 0.84 9.28E−03 3 12LYD299 0.98 1.37E−05 4 12 LYD299 0.85 7.82E−03 5 12 LYD300 0.80 1.68E−021 12 LYD300 0.75 3.08E−02 1 18 LYD300 0.73 6.21E−02 2 9 LYD300 0.866.54E−03 3 12 LYD300 0.78 2.26E−02 3 18 LYD301 0.73 3.94E−02 1 3 LYD3010.77 2.55E−02 1 7 LYD301 0.84 1.68E−02 2 4 LYD301 0.80 3.03E−02 2 3LYD301 0.77 4.39E−02 2 7 LYD301 0.71 4.99E−02 3 15 LYD301 0.89 3.27E−033 10 LYD301 0.71 5.06E−02 4 4 LYD301 0.72 4.21E−02 4 15 LYD301 0.801.82E−02 4 3 LYD301 0.78 2.24E−02 4 7 LYD301 0.76 2.94E−02 4 13 LYD3010.81 1.59E−02 5 4 LYD301 0.85 6.99E−03 5 15 LYD301 0.73 4.04E−02 5 5LYD302 0.83 2.04E−02 2 16 LYD302 0.74 5.73E−02 2 17 LYD302 0.91 1.50E−033 18 LYD302 0.76 2.85E−02 4 18 LYD303 0.83 1.00E−02 1 15 LYD303 0.762.83E−02 1 5 LYD303 0.72 4.40E−02 3 15 LYD303 0.87 5.08E−03 3 10 LYD3030.80 1.67E−02 4 18 LYD304 0.80 2.92E−02 2 2 LYD304 0.70 5.27E−02 3 3LYD305 0.93 2.70E−03 2 4 LYD305 0.83 2.01E−02 2 15 LYD305 0.73 6.26E−022 3 LYD305 0.76 2.94E−02 3 18 LYD306 0.87 4.65E−03 1 1 LYD306 0.866.39E−03 1 18 LYD306 0.74 5.59E−02 2 9 LYD306 0.82 1.34E−02 3 9 LYD3060.70 5.24E−02 3 10 LYD306 0.72 4.51E−02 4 1 LYD306 0.92 1.36E−03 5 18LYD307 0.89 2.95E−03 3 3 LYD307 0.79 1.94E−02 3 7 LYD308 0.74 3.52E−02 19 LYD308 0.71 7.45E−02 2 2 LYD308 0.70 5.29E−02 5 12 LYD308 0.975.57E−05 5 14 LYD308 0.76 2.86E−02 5 11 LYD308 0.86 6.25E−03 5 13 LYD3090.84 8.79E−03 3 16 LYD309 0.83 1.08E−02 4 1 LYD310 0.85 1.60E−02 2 12LYD310 0.74 5.68E−02 2 13 LYD310 0.95 3.36E−04 3 16 LYD310 0.73 4.17E−023 17 LYD310 0.75 3.39E−02 5 3 LYD310 0.91 1.78E−03 5 6 LYD310 0.874.96E−03 5 7 LYD311 0.73 4.06E−02 3 12 LYD311 0.80 1.76E−02 3 18 LYD3120.72 6.60E−02 2 18 LYD312 0.74 3.70E−02 3 12 LYD312 0.73 3.97E−02 5 18LYD313 0.75 3.13E−02 4 1 LYD313 0.87 4.72E−03 5 12 LYD315 0.83 2.12E−022 2 LYD315 0.73 6.03E−02 2 6 LYD315 0.72 4.45E−02 3 3 LYD315 0.811.41E−02 4 18 LYD316 0.76 4.96E−02 2 1 LYD316 0.79 3.36E−02 2 18 LYD3160.84 9.29E−03 3 3 LYD316 0.87 4.46E−03 3 7 LYD318 0.75 3.33E−02 5 2LYD319 0.77 4.30E−02 2 4 LYD319 0.84 1.83E−02 2 15 LYD319 0.77 4.11E−022 5 LYD319 0.78 2.17E−02 3 1 LYD319 0.75 3.34E−02 3 17 LYD319 0.857.55E−03 4 6 LYD319 0.76 2.92E−02 4 7 LYD320 0.74 3.49E−02 3 14 LYD3200.80 1.69E−02 3 13 LYD321 0.76 2.92E−02 4 1 LYD321 0.71 4.76E−02 5 17LYD322 0.87 4.62E−03 5 4 LYD322 0.79 2.07E−02 5 15 LYD323 0.70 5.23E−021 16 LYD323 0.77 4.25E−02 2 2 LYD323 0.73 4.15E−02 4 1 LYD323 0.874.54E−03 4 17 LYD323 0.92 1.17E−03 5 1 LYD323 0.85 8.20E−03 5 17 LYD3240.89 2.94E−03 3 12 LYD324 0.71 4.65E−02 3 18 LYD324 0.73 4.16E−02 5 4LYD324 0.82 1.18E−02 5 3 LYD324 0.74 3.52E−02 5 7 LYD325 0.81 1.55E−02 112 LYD325 0.75 3.21E−02 3 12 LYD325 0.77 2.52E−02 3 18 LYD326 0.772.60E−02 4 9 LYD326 0.73 3.87E−02 4 10 LYD327 0.78 2.35E−02 3 16 LYD3270.78 2.27E−02 5 18 LYD328 0.72 4.20E−02 3 3 LYD328 0.78 2.32E−02 5 12LYD328 0.89 2.68E−03 5 8 LYD329 0.71 4.80E−02 1 8 LYD329 0.79 3.41E−02 21 LYD329 0.92 3.64E−03 2 17 LYD329 0.78 2.25E−02 3 3 LYD329 0.743.57E−02 3 13 LYD329 0.81 1.41E−02 3 8 LYD329 0.90 2.51E−03 5 8 LYD3300.74 3.63E−02 3 2 LYD331 0.74 3.50E−02 1 6 LYD331 0.74 3.72E−02 1 7LYD331 0.72 4.38E−02 3 3 LYD331 0.76 2.77E−02 3 7 LYD331 0.73 3.85E−02 317 LYD331 0.75 3.29E−02 4 3 LYD331 0.75 3.36E−02 4 6 LYD331 0.811.54E−02 4 7 LYD331 0.75 3.15E−02 5 3 LYD331 0.76 3.00E−02 5 6 LYD3310.82 1.18E−02 5 7 LYD332 0.78 2.17E−02 1 6 LYD332 0.74 3.70E−02 3 16LYD332 0.81 1.45E−02 3 17 LYD334 0.72 6.61E−02 2 3 LYD334 0.82 2.30E−022 6 LYD334 0.80 3.09E−02 2 7 LYD334 0.76 4.96E−02 2 8 LYD334 0.782.19E−02 3 12 LYD334 0.73 4.01E−02 4 3 LYD334 0.70 5.27E−02 4 7 LYD3350.74 5.55E−02 2 2 LYD337 0.77 4.25E−02 2 10 LYD337 0.76 3.03E−02 3 3LYD338 0.75 3.38E−02 3 2 LYD338 0.74 3.55E−02 4 13 LYD338 0.82 1.31E−025 6 LYD338 0.79 1.88E−02 5 7 LYD339 0.79 3.58E−02 2 2 LYD339 0.714.83E−02 4 3 LYD339 0.78 2.13E−02 4 6 LYD339 0.80 1.71E−02 4 7 LYD3400.71 4.67E−02 1 8 LYD340 0.73 4.13E−02 4 3 LYD340 0.71 4.64E−02 4 7LYD340 0.84 9.57E−03 5 3 LYD340 0.74 3.42E−02 5 6 LYD340 0.89 3.32E−03 57 LYD341 0.86 1.40E−02 2 2 LYD341 0.76 2.91E−02 5 16 LYD341 0.715.05E−02 5 17 LYD342 0.71 7.17E−02 2 18 LYD342 0.88 4.16E−03 3 12 LYD3420.80 1.82E−02 4 13 LYD342 0.74 3.71E−02 5 4 LYD343 0.86 1.21E−02 2 2LYD343 0.77 2.57E−02 3 4 LYD343 0.72 4.25E−02 3 3 LYD343 0.83 1.12E−02 514 LYD343 0.70 5.19E−02 5 13 LYD344 0.77 2.43E−02 1 13 LYD344 0.812.69E−02 2 2 LYD344 0.74 3.70E−02 3 3 LYD344 0.86 6.81E−03 5 2 Table 5.Provided are the correlations (R) between the expression levels of yieldimproving genes and their homologues in tissues [roots, seeds, flower,and leaf; Expression sets (Exp)] and the phenotypic performance invarious yield, biomass, and direct yield components [Correlation IDvector (corr.)] under normal condition across Arabidopsis accessions. P= p value.

Example 3 Production of Arabidopsis Transcriptom and High ThroughputCorrelation Analysis of Normal and Nitrogen Limiting Conditions Using44K Arabidopsis Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis, the presentinventors utilized a Arabidopsis oligonucleotide micro-array, producedby Agilent Technologies [Hypertext Transfer Protocol://World Wide Web(dot) chem (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879].The array oligonucleotide represents about 44,000 Arabidopsis genes andtranscripts. To define correlations between the levels of RNA expressionwith NUE, yield components or vigor related parameters various plantcharacteristics of 14 different Arabidopsis ecotypes were analyzed.Among them, ten ecotypes encompassing the observed variance wereselected for RNA expression analysis. The correlation between the RNAlevels and the characterized parameters was analyzed using Pearsoncorrelation test [Hypertext Transfer Protocol://World Wide Web (dot)davidmlane (dot) com/hyperstat/A34739 (dot) html].

Experimental Procedures

Two tissues of plants [leaves and stems] growing at two differentnitrogen fertilization levels (1.5 mM Nitrogen or 6 mM Nitrogen) weresampled and RNA was extracted as described hereinabove under “GENERALEXPERIMENTAL AND BIOINFORMATICS METHODS”. For convenience, eachmicro-array expression information tissue type has received a Set ID assummarized in Table 6 below.

TABLE 6 Tissues used for Arabidopsis transcriptom expression setsExpression Set Set ID Leaves at 1.5 mM Nitrogen fertilization 1 Stems at6 mM Nitrogen fertilization 2 Leaves at 6 mM Nitrogen fertilization 3Stems at 1.5 mM Nitrogen fertilization 4 Provided are the identification(ID) digits of each of the Arabidopsis expression sets.

Assessment of Arabidopsis yield components and vigor related parametersunder different nitrogen fertilization levels—10 Arabidopsis accessionsin 2 repetitive plots each containing 8 plants per plot were grown atgreenhouse. The growing protocol used was as follows: surface sterilizedseeds were sown in Eppendorf tubes containing 0.5× Murashige-Skoog basalsalt medium and grown at 23° C. under 12-hour light and 12-hour darkdaily cycles for 10 days. Then, seedlings of similar size were carefullytransferred to pots filled with a mix of perlite and peat in a 1:1ratio. Constant nitrogen limiting conditions were achieved by irrigatingthe plants with a solution containing 1.5 mM inorganic nitrogen in theform of KNO₃, supplemented with 2 mM CaCl₂, 1.25 mM KH₂PO₄, 1.50 mMMgSO₄, 5 mM KCl, 0.01 mM H₃BO₃ and microelements, while normalirrigation conditions (Normal Nitrogen conditions) was achieved byapplying a solution of 6 mM inorganic nitrogen also in the form of KNO₃,supplemented with 2 mM CaCl₂, 1.25 mM KH₂PO₄, 1.50 mM MgSO₄, 0.01 mMH₃BO₃ and microelements. To follow plant growth, trays were photographedthe day nitrogen limiting conditions were initiated and subsequentlyevery 3 days for about 15 additional days. Rosette plant area was thendetermined from the digital pictures. ImageJ software was used forquantifying the plant size from the digital pictures [Hypertext TransferProtocol://rsb (dot) info (dot) nih (dot) govrij/] utilizing proprietaryscripts designed to analyze the size of rosette area from individualplants as a function of time. The image analysis system included apersonal desktop computer (Intel P4 3.0 GHz processor) and a publicdomain program—ImageJ 1.37 (Java based image processing program, whichwas developed at the U.S. National Institutes of Health and freelyavailable on the internet [Hypertext Transfer Protocol://rsbweb (dot)nih (dot) gov/]. Next, analyzed data was saved to text files andprocessed using the JMP statistical analysis software (SAS institute).

Data parameters collected are summarized in Table 7, herein below.

TABLE 7 Arabidopsis correlated parameters (vectors) CorrelationCorrelated parameter with ID N 6 mM; Seed Yield [gr./plant] 1 N 6 mM;Harvest Index (ratio) 2 N 6 mM; 1000 Seeds weight [gr.] 3 N 6 mM; seedyield/rosette area day at day 10 [gr./cm²] 4 N 6 mM; seed yield/leafblade [gr./cm²] 5 N 1.5 mM; Rosette Area at day 8 [cm²] 6 N 1.5 mM;Rosette Area at day 10 [cm²] 7 N 1.5 mM; Leaf Number at day 10 (number)8 N 1.5 mM; Leaf Blade Area at day 10 [cm²] 9 N 1.5 mM; RGR of RosetteArea at day 3 [cm²/day] 10 N 1.5 mM; t50 Flowering [day] 11 N 1.5 mM;Dry Weight [gr./plant] 12 N 1.5 mM; Seed Yield [gr./plant] 13 N 1.5 mM;Harvest Index (ratio) 14 N 1.5 mM; 1000 Seeds weight [gr.] 15 N 1.5 mM;seed yield/rosette area at day 10 [gr./cm²] 16 N 1.5 mM; seed yield/leafblade [gr./cm²] 17 N 1.5 mM; % Seed yield reduction 18 compared to N 6mM (ratio) N 1.5 mM; % Biomass reduction 19 compared to N 6 mM (ratio) N6 mM; Rosette Area at day 8 [cm²] 20 N 6 mM; Rosette Area at day 10[cm²] 21 N 6 mM; Leaf Number at day 10 (number) 22 N 6 mM; Leaf BladeArea at day 10 (cm²) 23 N 6 mM; RGR of Rosette Area at day 3 [cm²/gr.]24 N 6 mM; t50 Flowering [day] 25 N 6 mM; Dry Weight [gr./plant] 26 N 6mM; N level/DW (SPAD unit/gr. plant) 27 N 6 mM; DW/N level [gr./SPADunit] 28 N 6 mM; N level/FW (ratio) 29 N 6 mM; Seed yield/N unit[gr./SPAD unit] 30 N 1.5 mM; N level/FW [SPAD unit/gr.] 31 N 1.5 mM; Nlevel/DW [SPAD unit/gr.] 32 N 1.5 mM; DW/N level [gr/SPAD unit] 33 N 1.5mM; seed yield/N level [gr/SPAD unit] 34 Provided are the Arabidopsiscorrelated parameters (vectors). “N” = Nitrogen at the notedconcentrations; “gr.” = grams; “SPAD” = chlorophyll levels; “t50” = timewhere 50% of plants flowered; “gr./SPAD unit” = plant biomass expressedin grams per unit of nitrogen in plant measured by SPAD. “DW” = PlantDry Weight; “FW” = Plant Fresh weight; “N level/DW” = plant Nitrogenlevel measured in SPAD unit per plant biomass [gr.]; “DW/N level” =plant biomass per plant [gr.]/SPAD unit; Rosette Area (measured usingdigital analysis); Plot Coverage at the indicated day [%](calculated bythe dividing the total plant area with the total plot area); Leaf BladeArea at the indicated day [cm²] (measured using digital analysis); RGR(relative growth rate) of Rosette Area at the indicated day [cm²/day];t50 Flowering [day[(the day in which 50% of plant flower); seedyield/rosette area at day 10 [gr/cm²] (calculated); seed yield/leafblade [gr/cm²] (calculated); seed yield/N level [gr/SPAD unit](calculated).

Assessment of NUE, yield components and vigor-related parameters—TenArabidopsis ecotypes were grown in trays, each containing 8 plants perplot, in a greenhouse with controlled temperature conditions for about12 weeks. Plants were irrigated with different nitrogen concentration asdescribed above depending on the treatment applied. During this time,data was collected documented and analyzed. Most of chosen parameterswere analyzed by digital imaging.

Digital Imaging—Greenhouse Assay

An image acquisition system, which consists of a digital reflex camera(Canon EOS 400D) attached with a 55 mm focal length lens (Canon EF-Sseries) placed in a custom made Aluminum mount, was used for capturingimages of plants planted in containers within an environmentalcontrolled greenhouse. The image capturing process is repeated every 2-3days starting at day 9-12 till day 16-19 (respectively) fromtransplanting.

The image processing system which was used is described in Example 2above. Images were captured in resolution of 10 Mega Pixels (3888×2592pixels) and stored in a low compression JPEG (Joint Photographic ExpertsGroup standard) format. Next, image processing output data was saved totext files and analyzed using the JMP statistical analysis software (SASinstitute).

Leaf analysis—Using the digital analysis leaves data was calculated,including leaf number, leaf blade area, plot coverage, Rosette diameterand Rosette area.

Relative growth rate area: The relative growth rate area of the rosetteand the leaves was calculated according to Formulas VIII and IX,respectively.

Relative growth rate of rosette area=Regression coefficient of rosettearea along time course.  Formula VIII

Relative growth rate of plant leaf number=Regression coefficient ofplant leaf number along time course.  Formula IX

Seed yield and 1000 seeds weight—At the end of the experiment all seedsfrom all plots were collected and weighed in order to measure seed yieldper plant in terms of total seed weight per plant (gr.). For thecalculation of 1000 seed weight, an average weight of 0.02 grams wasmeasured from each sample, the seeds were scattered on a glass tray anda picture was taken. Using the digital analysis, the number of seeds ineach sample was calculated.

Dry weight and seed yield—At the end of the experiment, plant wereharvested and left to dry at 30° C. in a drying chamber. The biomass wasseparated from the seeds, weighed and divided by the number of plants.Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 30° C. in a drying chamber.

Harvest Index (seed)—The harvest index was calculated using Formula IVas described above [Harvest Index=Average seed yield per plant/Averagedry weight].

T₅₀ days to flowering—Each of the repeats was monitored for floweringdate. Days of flowering was calculated from sowing date till 50% of theplots flowered.

Plant nitrogen level—The chlorophyll content of leaves is a goodindicator of the nitrogen plant status since the degree of leafgreenness is highly correlated to this parameter. Chlorophyll contentwas determined using a Minolta SPAD 502 chlorophyll meter andmeasurement was performed at time of flowering. SPAD meter readings weredone on young fully developed leaf. Three measurements per leaf weretaken per plot. Based on this measurement, parameters such as the ratiobetween seed yield per nitrogen unit [seed yield/N level=seed yield perplant [gr.]/SPAD unit], plant DW per nitrogen unit [DW/N level=plantbiomass per plant [gr.]/SPAD unit], and nitrogen level per gram ofbiomass [N level/DW=SPAD unit/plant biomass per plant (gr.)] werecalculated.

Percent of seed yield reduction—measures the amount of seeds obtained inplants when grown under nitrogen-limiting conditions compared to seedyield produced at normal nitrogen levels expressed in percentages (%).

Experimental Results

10 different Arabidopsis accessions (ecotypes) were grown andcharacterized for 37 parameters as described above. The average for eachof the measured parameters was calculated using the JMP software (Table8 and 9 below). Subsequent correlation analysis between the varioustranscriptom sets (Table 6) and the average parameters was conducted(Table 10).

TABLE 8 Measured parameters in Arabidopsis accessions Ecotype/ Corr. IDLine-1 Line-2 Line-3 Line-4 Line-5 1 0.11575 0.1651625 0.108468750.08195 0.11918125 2 0.27999946 0.30852795 0.28360337 0.158357490.2058752 3 0.01474256 0.01686869 0.01776982 0.01207785 0.01553451 40.08243942 0.10579199 0.04051086 0.03389743 0.05563382 5 0.339197610.52646 0.20718176 0.18267073 0.27723756 6 0.76004675 0.708788921.06135087 1.1569617 1.0001808 7 1.42963825 1.32500951 1.76624241.97095367 1.83234886 8 6.875 7.3125 7.3125 7.875 7.75 9 0.334865160.26631535 0.37431832 0.3868142 0.3699387 10 0.63055011 0.79278940.50199713 0.49086784 0.71950821 11 15.9674256 20.967741 14.835643324.7083342 23.6981965 12 0.164375 0.12375 0.081875 0.113125 0.12375 130.0317625 0.02526875 0.0230125 0.0098375 0.00879375 14 0.192210060.20271686 0.29498642 0.08498642 0.07117143 15 0.0164661 0.015755860.01752601 0.01428241 0.02237168 16 0.0221105 0.0190193 0.013565050.00522479 0.00495957 17 0.09480609 0.09462778 0.06338215 0.026395710.02415312 18 72.55939525 84.70067358 78.78421204 87.9957291 92.6215323319 60.74626866 76.70588235 78.55973813 78.14009662 78.6407767 200.75895075 0.85681934 1.4770776 1.27750001 1.09516034 21 1.405947071.57034299 2.67253089 2.41758766 2.14203082 22 6.25 7.3125 8.0625 8.758.75 23 0.34248457 0.31479663 0.52295373 0.44862141 0.42970295 240.6891365 1.02385276 0.61434467 0.60098475 0.65076159 25 16.371401920.5000004 14.6346459 24 23.5950703 26 0.41875 0.53125 0.381875 0.51750.579375 27 22.49 28.27 28 0.018620067 0.018306704 29 53.7054984854.62479871 30 0.004209091 0.002952562 31 45.59 42.11 32 167.3003802241.0607735 33 0.005977273 0.004148331 34 0.001155 0.000360744 Providedare the values of each of the parameters measured in Arabidopsisecotypes (lines 1-5) using the correlation ID numbers described in Table7 hereinabove.

TABLE 9 Measured parameters in Arabidopsis accessions-continue Ecotype/Corr. ID Line-6 Line-7 Line-8 Line-9 Line-10 1 0.13876875 0.106956250.1380875 0.0948125 0.06754375 2 0.2762645 0.17062181 0.212480360.1655574 0.13618211 3 0.01543419 0.01403759 0.01660137 0.016080780.01601005 4 0.05702681 0.05537429 0.05071512 0.05818119 0.03071849 50.28118206 0.25233196 0.27125843 0.23547195 0.15792361 6 0.910497140.94164552 1.11820707 0.63830722 0.99598092 7 1.81767559 1.636225871.99606088 1.14962099 1.75392334 8 7.625 7.1875 8.625 5.92857143 7.93759 0.38633196 0.34966412 0.37896098 0.30665846 0.37272108 10 0.825227260.64561797 0.66798775 0.63647393 0.60534304 11 18.0593189 19.48818423.5678247 21.8884261 23.5662586 12 0.134375 0.10625 0.148125 0.171250.18375 13 0.03231875 0.01931875 0.0120125 0.01350446 0.005525 140.24052391 0.1786763 0.08141143 0.07930284 0.03089076 15 0.01478970.01364492 0.0216896 0.01860767 0.01834821 16 0.01780867 0.012738050.00676616 0.01177002 0.00315298 17 0.08363306 0.05886 0.034307770.04403838 0.01485086 18 76.71035446 81.93770818 91.30080565 85.7566671191.82011659 19 73.19201995 83.06772908 77.18960539 70.1199563862.97229219 20 1.23563711 1.09369169 1.40984007 0.89057621 1.22408964 212.4744351 1.96527638 2.72071991 1.64211359 2.20715087 22 8.375 7.1259.4375 6.3125 8.0625 23 0.49679143 0.42802388 0.50868963 0.405314710.43015889 24 0.67559702 0.58421861 0.61299718 0.51546854 0.47694692 2515.032695 19.7496866 22.8871401 18.8041534 23.3779994 26 0.50125 0.62750.649375 0.573125 0.49625 27 33.32 39 17.64 28 0.015042326 0.0146942820.028130951 29 66.4790786 68.05368458 35.54803406 30 0.0052987640.003255054 0.00233267 31 53.11 67 28.15 32 194.9767442 169.3430657157.8231293 33 0.005128817 0.005905172 0.006336207 34 0.001233540.000465671 0.000190517 Provided are the values of each of theparameters measured in Arabidopsis ecotypes (lines 6-10) using thecorrelation ID numbers described in Table 7 hereinabove.

TABLE 10 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal or abiotic stress conditions across Arabidopsisaccessions Gene Exp. Corr. Gene Exp. Corr. Name R P value set ID Name RP value set ID LYD289 0.74 1.36E−02 1 19 LYD289 0.72 2.76E−02 2 19LYD289 0.76 1.02E−02 3 19 LYD289 0.71 2.17E−02 4 19 LYD290 0.78 8.04E−031 2 LYD290 0.70 2.34E−02 1 1 LYD290 0.74 1.53E−02 3 20 LYD290 0.814.63E−03 3 9 LYD290 0.77 9.60E−03 3 21 LYD290 0.86 1.41E−03 3 23 LYD2910.74 2.25E−02 2 2 LYD291 0.79 1.13E−02 2 16 LYD291 0.73 2.44E−02 2 4LYD291 0.81 8.40E−03 2 17 LYD291 0.71 3.28E−02 2 14 LYD291 0.76 1.10E−023 16 LYD291 0.76 1.08E−02 3 13 LYD292 0.74 1.38E−02 3 16 LYD292 0.731.65E−02 3 17 LYD292 0.75 1.17E−02 3 13 LYD292 0.92 2.05E−04 3 14 LYD2930.82 3.60E−03 1 11 LYD293 0.77 8.67E−03 1 25 LYD293 0.81 4.43E−03 1 18LYD293 0.86 2.95E−03 2 8 LYD294 0.71 2.05E−02 1 2 LYD294 0.84 2.53E−03 116 LYD294 0.85 1.76E−03 1 17 LYD294 0.84 2.49E−03 1 13 LYD294 0.751.18E−02 1 14 LYD294 0.70 2.41E−02 3 2 LYD294 0.72 1.94E−02 3 17 LYD2940.81 4.93E−03 3 13 LYD295 0.93 8.65E−05 1 11 LYD295 0.89 5.39E−04 1 25LYD295 0.87 1.15E−03 1 18 LYD295 0.73 1.76E−02 3 25 LYD296 0.71 2.28E−021 23 LYD297 0.73 1.58E−02 1 16 LYD297 0.78 7.28E−03 1 13 LYD300 0.732.51E−02 2 22 LYD303 0.70 2.39E−02 1 17 LYD303 0.72 1.91E−02 1 13 LYD3030.77 9.48E−03 3 2 LYD303 0.76 1.11E−02 3 17 LYD303 0.83 2.91E−03 3 13LYD303 0.73 1.73E−02 3 14 LYD304 0.70 2.34E−02 1 14 LYD304 0.72 1.84E−023 24 LYD308 0.78 8.33E−03 4 6 LYD309 0.72 1.82E−02 1 20 LYD310 0.761.10E−02 1 20 LYD310 0.73 1.65E−02 1 21 LYD310 0.72 1.82E−02 1 23 LYD3150.88 8.81E−04 1 2 LYD315 0.82 3.42E−03 1 16 LYD315 0.84 2.10E−03 1 17LYD315 0.84 2.42E−03 1 13 LYD315 0.79 6.32E−03 1 14 LYD315 0.70 3.57E−022 2 LYD315 0.70 3.52E−02 2 13 LYD315 0.79 1.05E−02 2 14 LYD315 0.787.74E−03 3 16 LYD315 0.86 1.43E−03 3 4 LYD315 0.75 1.22E−02 3 17 LYD3150.75 1.33E−02 3 5 LYD315 0.91 2.42E−04 4 2 LYD315 0.75 1.27E−02 4 16LYD315 0.78 7.43E−03 4 17 LYD315 0.77 9.03E−03 4 13 LYD315 0.81 4.26E−034 14 LYD318 0.78 7.45E−03 1 2 LYD318 0.86 1.26E−03 1 1 LYD318 0.751.22E−02 1 5 LYD318 0.86 1.36E−03 1 24 LYD318 0.71 2.14E−02 3 16 LYD3180.74 1.35E−02 3 17 LYD318 0.77 9.45E−03 3 1 LYD318 0.76 1.01E−02 3 13LYD318 0.72 1.95E−02 3 14 LYD319 0.74 1.41E−02 4 15 LYD320 0.81 4.38E−031 2 LYD320 0.76 1.10E−02 1 13 LYD320 0.79 6.15E−03 1 14 LYD320 0.722.73E−02 2 2 LYD320 0.81 8.30E−03 2 4 LYD320 0.79 1.20E−02 2 5 LYD3200.78 1.33E−02 2 24 LYD320 0.78 8.46E−03 3 2 LYD320 0.78 8.03E−03 4 13LYD320 0.90 3.95E−04 4 14 LYD322 0.72 1.91E−02 1 11 LYD322 0.74 1.43E−021 18 LYD323 0.72 1.95E−02 3 2 LYD325 0.86 1.24E−03 3 11 LYD325 0.871.22E−03 3 25 LYD325 0.94 6.39E−05 3 18 LYD327 0.79 6.01E−03 1 2 LYD3270.83 2.81E−03 1 16 LYD327 0.81 4.37E−03 1 17 LYD327 0.92 1.95E−04 1 13LYD327 0.81 4.43E−03 1 14 LYD327 0.83 5.30E−03 2 14 LYD327 0.80 5.34E−034 2 LYD327 0.84 2.31E−03 4 16 LYD327 0.84 2.56E−03 4 17 LYD327 0.921.27E−04 4 13 LYD327 0.90 3.59E−04 4 14 LYD330 0.75 2.05E−02 2 3 LYD3310.74 1.36E−02 1 22 LYD331 0.81 4.46E−03 1 20 LYD331 0.70 2.28E−02 1 6LYD331 0.81 4.34E−03 1 21 LYD331 0.70 2.39E−02 1 7 LYD331 0.77 9.77E−031 23 LYD331 0.75 1.92E−02 2 19 LYD331 0.78 1.34E−02 2 20 LYD331 0.761.78E−02 2 21 LYD331 0.71 3.20E−02 2 23 LYD331 0.74 1.36E−02 3 20 LYD3310.74 1.35E−02 3 21 LYD331 0.87 1.02E−03 4 19 LYD332 0.86 1.42E−03 1 16LYD332 0.82 3.66E−03 1 17 LYD332 0.90 3.17E−04 1 13 LYD332 0.79 6.66E−031 14 LYD332 0.81 4.49E−03 4 16 LYD332 0.80 4.97E−03 4 17 LYD332 0.796.44E−03 4 13 LYD334 0.73 2.65E−02 2 6 LYD335 0.71 2.19E−02 1 2 LYD3350.79 6.85E−03 1 16 LYD335 0.78 8.37E−03 1 17 LYD335 0.73 1.70E−02 1 13LYD335 0.72 1.85E−02 1 14 LYD335 0.72 1.97E−02 3 1 LYD337 0.76 1.07E−024 4 LYD337 0.77 9.01E−03 4 5 LYD339 0.71 2.23E−02 3 10 LYD339 0.788.08E−03 3 26 LYD340 0.77 9.66E−03 3 18 LYD340 0.85 1.69E−03 3 15 LYD3410.76 1.10E−02 3 20 LYD341 0.78 7.19E−03 3 21 LYD341 0.85 1.62E−03 3 23LYD344 0.80 5.20E−03 1 14 LYD344 0.74 1.49E−02 3 14 Table 10. Providedare the correlations (R) between the expression levels of yieldimproving genes and their homologues in tissues [Leaves or stems;Expression sets (Exp)] and the phenotypic performance in various yield,biomass, growth rate and/or vigor components [Correlation vector(corr.)] under stress conditions or normal conditions across Arabidopsisaccessions. P = p value.

Example 4 Production of Tomato Transcriptom and High ThroughputCorrelation Analysis Using 44K Tomato Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis between NUErelated phenotypes and gene expression, the present inventors utilized aTomato oligonucleotide micro-array, produced by Agilent Technologies[Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent(dot) com/Scripts/PDS (dot) asp?lPage=50879]. The array oligonucleotiderepresents about 44,000 Tomato genes and transcripts. In order to definecorrelations between the levels of RNA expression with NUE, ABST, yieldcomponents or vigor related parameters various plant characteristics of18 different Tomato varieties were analyzed. Among them, 10 varietiesencompassing the observed variance were selected for RNA expressionanalysis. The correlation between the RNA levels and the characterizedparameters was analyzed using Pearson correlation test [HypertextTransfer Protocol://World Wide Web (dot) davidmlane (dot)com/hyperstat/A34739 (dot) html].

Correlation of Tomato Varieties Across Ecotypes Grown Under LowNitrogen, Drought and Regular Growth Conditions Experimental procedures:

10 Tomato varieties were grown in 3 repetitive blocks, each containing 6plants per plot were grown at net house. Briefly, the growing protocolwas as follows:

1. Regular growth conditions: Tomato varieties were grown under normalconditions (4-6 Liters/m² of water per day and fertilized with NPK asrecommended in protocols for commercial tomato production).

2. Low Nitrogen fertilization conditions: Tomato varieties were grownunder normal conditions (4-6 Liters/m² per day and fertilized with NPKas recommended in protocols for commercial tomato production) untilflower stage. At this time, Nitrogen fertilization was stopped.

3. Drought stress: Tomato variety was grown under normal conditions (4-6Liters/m² per day) until flower stage. At this time, irrigation wasreduced to 50% compared to normal conditions. Plants were phenotyped ona daily basis following the standard descriptor of tomato (Table 12).Harvest was conducted while 50% of the fruits were red (mature). Plantswere separated to the vegetative part and fruits, of them, 2 nodes wereanalyzed for additional inflorescent parameters such as size, number offlowers, and inflorescent weight. Fresh weight of all vegetativematerial was measured. Fruits were separated to colors (red vs. green)and in accordance with the fruit size (small, medium and large). Next,analyzed data was saved to text files and processed using the JMPstatistical analysis software (SAS institute). Data parameters collectedare summarized in Tables 13-15, herein below.

Analyzed Tomato tissues—Two tissues at different developmental stages[flower and leaf], representing different plant characteristics, weresampled and RNA was extracted as described above. For convenience, eachmicro-array expression information tissue type has received a Set ID assummarized in Table 11 below.

TABLE 11 Tomato transcriptom expression sets Expression Set Set ID Leafat reproductive stage under NUE conditions  1 + 10 Flower under normalconditions 5 + 2 Leaf at reproductive stage under normal conditions 8 +3 Flower under drought conditions 9 + 7 Leaf at reproductive stage underdrought conditions 11 + 4  Flower under NUE conditions 12 + 6  Providedare the identification (ID) digits of each of the tomato expressionsets.

Table 12 provides the tomato correlated parameters (Vectors). Theaverage for each of the measured parameters was calculated using the JMPsoftware and values are summarized in Tables 13-15 below. Subsequentcorrelation analysis was conducted. Results were integrated to thedatabase (Table 16).

TABLE 12 Tomato correlated parameters (vectors) Correlated parameterwith Correlation ID NUE [yield/SPAD] (Normal) 1 NUpE [biomass/SPAD](Normal) 2 HI [yield/yield + biomass] (Normal) 3 NUE2 biomass/SPAD](Normal) 4 Total Leaf Area [cm²] (Normal) 5 Leaflet Length [cm] (Normal)6 Leaflet Width (Normal) 7 100 weight green fruit (Normal) 8 100 weightred fruit (Normal) 9 SLA [leaf area/plant biomass] (Normal) 10Yield/total leaf area (Normal) 11 Yield/SLA (Normal) 12 FruitYield/Plant (NUE) 13 FW/Plant (NUE) 14 average red fruit weight (NUE) 15Fruit NUE/Normal 16 FW NUE/Normal 17 SPAD NUE 18 RWC NUE 19 SPAD 100%RWC (NUE) 20 SPAD NUE/Normal 21 SAPD 100% RWC NUE/Normal 22 RWCNUE/Normal 23 No flowers (NUE) 24 Weight clusters (flowers) (NUE) 25Num. Flowers NUE/Normal 26 Cluster Weight NUE/Normal 27 RWC Drought 28RWC Drought/Normal 29 Num of flowers (Drought) 30 Weight flower clusters(Drought) 31 Num of Flower Drought/Normal 32 Num of Flower Drought/NUE33 flower cluster weight Drought/Normal 34 flower cluster weightDrought/NUE 35 Fruit Yield/Plant Drought 36 FW/Plant Drought 37 averagered fruit weight Drought 38 Fruit Yield Drought/Normal 39 FruitDrought/NUE 40 FW drought/Normal 41 red fruit weight Drought/Normal 42Fruit yield/Plant (Normal) 43 FW/Plant (Normal) 44 average red fruitweight (Normal) 45 SPAD (Normal) 46 RWC (Normal) 47 SPAD 100% RWC(Normal) 48 No flowers (Normal) 49 Weight Flower clusters (Normal) 50Total Leaf Area [cm²]) (Drought) 51 Leaflet Length [cm]) (Drought) 52Leaflet Width [cm] (Drought) 53 100 weight green fruit (Drought) 54 100weight red fruit (Drought) 55 NUE [yield/SPAD] (Low N) 56 NUpE[biomass/SPAD] (Low N) 57 HI [yield/yield + biomass] (Low N) 58 NUE2biomass/SPAD] (Low N) 59 Total Leaf Area [cm²] (Low N) 60 Leaflet Length[cm] (Low N) 61 Leaflet Width (Low N) 62 100 weight green fruit (Low N)63 SLA [leaf area/plant biomass] (Low N) 64 Yield/total leaf area (LowN) 65 Yield/SLA (Low N) 66 100 weight red fruit (Low N) 67 Provided arethe tomato correlated parameters. “gr.” = grams; “FW” = fresh weight;“NUE” = nitrogen use efficiency; “RWC” = relative water content; “NUpE”= nitrogen uptake efficiency; “SPAD” = chlorophyll levels; “HI” =harvest index (vegetative weight divided on yield); “SLA” = specificleaf area (leaf area divided by leaf dry weight), Treatment in theparenthesis.

Fruit Weight (grams)—At the end of the experiment [when 50% of thefruits were ripe (red)] all fruits from plots within blocks A-C werecollected. The total fruits were counted and weighted. The averagefruits weight was calculated by dividing the total fruit weight by thenumber of fruits.

Plant vegetative Weight (grams)—At the end of the experiment [when 50%of the fruit were ripe (red)] all plants from plots within blocks A-Cwere collected. Fresh weight was measured (grams).

Inflorescence Weight (grams)—At the end of the experiment [when 50% ofthe fruits were ripe (red)] two Inflorescence from plots within blocksA-C were collected. The Inflorescence weight (gr.) and number of flowersper inflorescence were counted.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed at time of flowering.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken per plot.

Water use efficiency (WUE)—can be determined as the biomass produced perunit transpiration. To analyze WUE, leaf relative water content wasmeasured in control and transgenic plants. Fresh weight (FW) wasimmediately recorded; then leaves were soaked for 8 hours in distilledwater at room temperature in the dark, and the turgid weight (TW) wasrecorded. Total dry weight (DW) was recorded after drying the leaves at60° C. to a constant weight. Relative water content (RWC) was calculatedaccording to the following Formula I [(FW−DW/TW−DW)×100] as describedabove.

Plants that maintain high relative water content (RWC) compared tocontrol lines were considered more tolerant to drought than thoseexhibiting reduced relative water content.

Experimental Results

TABLE 13 Measured parameters in Tomato accessions (lines 1-6) Ecotype/Correlation ID No. Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 1 0.02 0.010.01 0.00 0.01 0.01 2 0.03 0.09 0.05 0.02 0.05 0.05 3 0.35 0.10 0.140.12 0.18 0.19 4 0.05 0.09 0.06 0.02 0.06 0.06 5 426.10 582.38 291.40593.58 6 6.34 7.99 5.59 7.70 7 3.69 4.77 3.43 4.56 8 0.56 3.05 0.24 2.589 0.82 2.46 0.50 2.76 10 140.99 689.67 130.22 299.12 11 0.00 0.00 0.000.00 12 0.00 0.00 0.00 0.00 13 0.41 0.66 0.48 0.46 1.35 0.35 14 4.041.21 2.25 2.54 1.85 3.06 15 0.02 0.19 0.01 0.01 0.10 0.00 16 0.49 1.930.97 3.80 2.78 0.78 17 2.65 0.38 0.74 3.01 0.83 1.54 18 38.40 39.4047.50 37.00 44.60 41.70 19 74.07 99.08 69.49 63.24 77.36 77.91 20 28.4739.04 33.01 23.42 34.53 32.51 21 0.77 1.06 0.85 0.80 0.93 0.96 22 0.791.37 0.92 0.75 1.31 0.97 23 1.02 1.30 1.08 0.94 1.41 1.00 24 19.00 5.339.00 13.00 10.67 16.67 25 0.53 0.37 0.31 0.35 0.47 0.25 26 3.35 0.281.42 1.70 1.10 2.00 27 0.46 1.07 0.44 0.01 1.08 0.02 28 72.12 74.5165.33 72.22 66.13 68.33 29 0.99 0.97 1.02 1.08 1.21 0.88 30 16.67 6.5015.67 20.33 11.67 25.33 31 0.37 0.41 0.33 0.29 0.55 0.31 32 2.94 0.342.47 2.65 1.21 3.04 33 0.88 1.22 1.74 1.56 1.09 1.52 34 0.32 1.19 0.470.01 1.25 0.03 35 0.69 1.11 1.06 0.82 1.16 1.25 36 0.47 0.48 0.63 0.352.04 0.25 37 2.62 1.09 1.85 2.22 2.63 2.71 38 0.01 0.19 0.21 0.00 0.100.00 39 0.57 1.41 1.27 2.88 4.20 0.55 40 1.15 0.73 1.32 0.76 1.51 0.7141 1.72 0.34 0.61 2.63 1.18 1.36 42 0.19 24.37 25.38 0.02 20.26 0.04 430.83 0.34 0.49 0.12 0.49 0.45 44 1.53 3.17 3.02 0.84 2.24 1.98 45 0.050.01 0.01 0.29 0.01 0.05 46 49.70 37.20 55.80 46.40 48.20 43.40 47 72.8376.47 64.29 67.07 54.79 77.61 48 36.17 28.45 35.89 31.09 26.38 33.68 495.67 19.33 6.33 7.67 9.67 8.33 50 1.17 0.34 0.69 56.35 0.44 11.31 560.01 0.02 0.01 0.02 0.04 0.01 57 0.14 0.03 0.07 0.11 0.05 0.09 58 0.090.35 0.18 0.15 0.42 0.10 59 0.16 0.05 0.08 0.13 0.09 0.11 60 565.93384.77 294.83 378.00 476.39 197.08 61 6.40 5.92 3.69 5.43 6.95 3.73 623.47 1.97 1.79 2.55 3.52 1.73 63 0.87 3.66 0.57 0.37 3.40 0.68 64 140.04317.12 131.29 148.82 257.51 64.34 65 0.00 0.00 0.00 0.00 0.00 0.00 660.00 0.00 0.00 0.00 0.01 0.01 67 1.06 6.87 0.65 0.53 7.17 0.44 Table 13.Provided are the values of each of the parameters (as described above inTable 12) measured in tomato accessions (Line number) under all growthconditions. Growth conditions are specified in the experimentalprocedure section.

TABLE 14 Measured parameters in Tomato accessions (lines 7-12)Ecotype/Correlation ID No. Line-7 Line-8 Line-9 Line-10 Line-11 Line-121 0.01 0.01 0.00 0.01 0.02 0.00 2 0.02 0.04 0.05 0.05 0.05 0.08 3 0.380.17 0.06 0.10 0.27 0.05 4 0.03 0.05 0.06 0.06 0.06 0.08 5 947.59 233.35340.73 339.11 190.14 421.79 6 7.85 6.22 6.16 5.65 4.39 4.44 7 4.44 3.153.37 3.13 2.40 2.02 8 6.32 5.75 0.38 0.30 1.95 2.53 9 5.32 5.24 0.610.66 2.70 0.70 10 1117.74 111.77 106.29 123.14 104.99 111.88 11 0.000.00 0.00 0.00 0.00 0.00 12 0.00 0.00 0.00 0.00 0.01 0.00 13 0.01 0.510.44 0.47 1.59 0.39 14 3.13 2.54 1.84 1.52 1.91 1.86 15 0.01 0.01 0.010.01 0.02 0.01 16 0.02 1.16 2.07 1.51 2.41 2.06 17 3.70 1.22 0.58 0.551.06 0.49 18 34.40 50.00 44.70 53.70 35.70 58.80 19 80.49 67.40 67.1666.07 69.57 69.30 20 27.66 33.68 30.04 35.50 24.81 40.77 21 0.80 0.940.76 1.05 0.89 1.24 22 1.11 0.95 0.79 0.92 0.94 1.36 23 1.38 1.01 1.040.88 1.05 1.10 24 6.00 16.00 15.00 6.00 17.00 13.00 25 0.29 0.47 0.400.30 0.82 0.40 26 1.20 1.92 1.50 0.86 1.89 1.63 27 0.37 0.81 0.55 0.360.95 0.80 28 78.13 18.46 73.21 62.50 67.21 75.76 29 1.34 0.28 1.13 0.831.01 1.20 30 29.73 17.33 14.67 29.67 15.00 10.33 31 0.45 0.56 0.30 0.310.31 0.31 32 5.95 2.08 1.47 4.24 1.67 1.29 33 4.96 1.08 0.98 4.94 0.880.79 34 0.56 0.96 0.42 0.38 0.36 0.62 35 1.52 1.19 0.76 1.04 0.38 0.7836 0.05 0.45 0.29 1.02 0.60 0.49 37 3.41 2.11 1.95 1.76 1.72 1.92 380.03 0.01 0.01 0.00 0.01 0.01 39 0.09 1.03 1.39 3.28 0.91 2.62 40 5.060.89 0.67 2.17 0.38 1.27 41 4.02 1.01 0.61 0.64 0.95 0.51 42 0.15 0.020.86 0.74 0.09 1.72 43 0.53 0.44 0.21 0.31 0.66 0.19 44 0.85 2.09 3.212.75 1.81 3.77 45 0.23 0.29 0.01 0.01 0.06 0.01 46 42.90 53.30 58.5051.10 40.00 47.60 47 58.18 66.51 64.71 75.25 66.23 63.21 48 24.98 35.4737.87 38.43 26.49 30.07 49 5.00 8.33 10.00 7.00 9.00 8.00 50 0.79 0.580.73 0.83 0.86 0.50 51 337.63 52 5.15 53 2.55 54 0.80 55 0.89 56 0.000.02 0.01 0.01 0.06 0.01 57 0.11 0.08 0.06 0.04 0.08 0.05 58 0.00 0.170.19 0.24 0.45 0.17 59 0.11 0.09 0.08 0.06 0.14 0.06 60 453.24 625.51748.01 453.96 164.85 338.30 61 4.39 6.72 6.66 4.39 3.90 5.29 62 1.873.54 3.28 2.52 2.61 2.61 63 0.45 0.47 0.54 0.39 0.97 0.91 64 144.60246.05 405.55 299.32 86.19 182.32 65 0.00 0.00 0.00 0.00 0.01 0.00 660.00 0.00 0.00 0.00 0.02 0.00 67 0.55 0.75 0.58 1.27 1.34 Table 14.Provided are the values of each of the parameters (as described above inTable 12) measured in tomato accessions (Line number) under all growthconditions. Growth conditions are specified in the experimentalprocedure section.

TABLE 15 Measured parameters in Tomato accessions (lines 13-18)Ecotype/Correlation ID No. Line-13 Line-14 Line-15 Line-16 Line-17Line-18 1 0.01 0.01 0.01 0.01 0.01 0.00 2 0.03 0.04 0.05 0.03 0.07 0.043 0.31 0.12 0.14 0.17 0.09 0.11 4 0.05 0.05 0.06 0.04 0.08 0.04 5 581.33807.51 784.06 351.80 255.78 1078.10 6 6.77 7.42 6.71 5.87 4.16 10.29 73.80 3.74 2.98 3.22 2.09 5.91 8 1.42 2.03 1.39 2.27 0.45 0.42 9 2.644.67 2.17 0.49 0.34 0.75 10 307.95 419.37 365.81 212.93 84.94 469.87 110.00 0.00 0.00 0.00 0.00 0.00 12 0.00 0.00 0.00 0.00 0.00 0.00 13 0.320.45 0.14 0.40 1.44 0.50 14 2.47 2.62 1.08 1.17 0.92 1.09 15 0.01 0.050.36 0.04 0.63 16 0.38 1.64 0.41 1.21 4.59 1.70 17 1.31 1.36 0.51 0.710.31 0.47 18 47.50 45.20 39.00 45.00 65.30 51.90 19 100.00 57.66 90.7968.00 59.65 72.17 20 47.47 26.06 35.38 30.60 38.97 37.46 21 0.82 0.940.89 0.83 1.57 0.88 22 1.44 1.50 1.05 0.56 1.48 0.84 23 1.76 1.60 1.170.68 0.94 0.96 24 8.67 9.33 12.67 6.67 9.33 8.00 25 0.35 0.43 0.35 0.450.28 0.47 26 1.63 1.17 1.65 0.74 0.88 0.89 27 0.34 0.61 0.94 0.68 0.401.44 28 62.82 70.69 55.75 75.22 63.68 62.31 29 1.11 1.97 0.72 0.75 1.010.83 30 18.33 12.00 20.33 12.67 12.67 11.33 31 8.36 0.29 0.34 0.44 0.270.43 32 3.44 1.50 2.65 1.41 1.19 1.26 33 2.12 1.29 1.61 1.90 1.36 1.4234 8.20 0.41 0.91 0.67 0.38 1.31 35 24.12 0.67 0.97 0.99 0.95 0.91 360.27 0.68 0.14 0.53 0.55 0.41 37 2.21 3.73 0.75 1.76 0.63 1.11 38 0.000.01 0.30 0.14 0.04 0.09 39 0.32 2.48 0.41 1.62 1.76 1.42 40 0.84 1.510.98 1.34 0.38 0.84 41 1.17 1.94 0.35 1.06 0.21 0.48 42 0.17 0.02 10.5027.89 11.79 9.98 43 0.85 0.27 0.35 0.33 0.31 0.29 44 1.89 1.93 2.14 1.653.01 2.29 45 0.03 0.26 0.03 0.00 0.00 0.01 46 57.90 48.30 43.60 54.5041.60 59.10 47 56.77 35.96 77.62 100.00 63.16 75.13 48 32.89 17.35 33.8254.47 26.25 44.43 49 5.33 8.00 7.67 9.00 10.67 9.00 50 1.02 0.70 0.380.66 0.70 0.33 51 130.78 557.93 176.67 791.86 517.05 832.27 51 3.38 7.145.48 8.62 6.35 6.77 53 2.04 4.17 3.09 4.69 3.87 2.91 54 0.28 0.38 0.632.86 1.16 4.40 55 0.35 0.63 2.27 7.40 2.94 11.60 56 0.01 0.02 0.00 0.010.04 0.01 57 0.05 0.10 0.03 0.04 0.02 0.03 58 0.12 0.15 0.12 0.25 0.610.31 59 0.06 0.12 0.03 0.05 0.06 0.04 60 396.00 236.15 174.58 441.78489.18 707.80 61 6.32 5.11 4.72 6.83 7.10 8.21 62 3.58 2.56 2.48 3.433.30 3.69 63 0.36 0.35 0.57 4.38 2.02 8.13 64 160.18 90.10 160.99 379.03531.08 650.68 65 0.00 0.00 0.00 0.00 0.00 0.00 66 0.00 0.00 0.00 0.000.00 0.00 67 0.52 0.57 0.94 6.17 3.67 11.33 Table 15: Provided are thevalues of each of the parameters (as described above in Table 12)measured in tomato accessions (Line number) under all growth conditions.Growth conditions are specified in the experimental procedure section.

TABLE 16 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal and stress conditions across tomato ecotypesGene Exp. Corr. Gene Exp. Corr. Name R P value set ID Name R P value setID LYD475 0.71 2.04E−02 1 20 LYD475 0.79 6.15E−03 1 22 LYD475 0.772.51E−02 2 12 LYD475 0.75 3.15E−02 2 11 LYD475 0.73 1.61E−02 12 19LYD477 0.87 9.33E−04 1 20 LYD477 0.88 3.84E−03 2 12 LYD477 0.84 9.63E−032 11 LYD477 0.81 4.38E−03 11 35 LYD477 0.80 5.67E−03 11 34 LYD477 0.814.78E−03 11 31 LYD478 0.73 1.69E−02 1 20 LYD478 0.83 5.37E−03 2 3 LYD4780.85 4.01E−03 2 1 LYD478 0.76 2.79E−02 2 9 LYD478 0.88 1.78E−03 3 1LYD478 0.86 1.59E−03 9 35 LYD478 0.83 2.72E−03 9 34 LYD478 0.85 1.69E−039 31 LYD478 0.88 8.98E−04 12 20 LYD478 0.73 1.76E−02 12 23 LYD478 0.823.55E−03 12 19 LYD479 0.80 1.76E−02 2 11 LYD479 0.73 1.63E−02 6 59LYD479 0.75 1.17E−02 6 57 LYD479 0.77 9.70E−03 9 33 LYD479 0.75 1.24E−029 30 LYD479 0.74 1.37E−02 12 14 LYD479 0.83 3.23E−03 12 17 LYD479 0.778.56E−03 12 26 LYD479 0.71 2.25E−02 11 33 LYD479 0.76 1.10E−02 11 40LYD480 0.92 4.80E−04 3 3 LYD480 0.81 8.33E−03 3 1 LYD480 0.74 1.36E−02 846 LYD481 0.89 1.16E−03 2 3 LYD481 0.94 1.51E−04 2 1 LYD481 0.821.18E−02 2 9 LYD481 0.78 1.41E−02 3 4 LYD482 0.73 4.01E−02 2 12 LYD4820.81 1.41E−02 2 11 LYD482 0.76 1.13E−02 5 46 LYD482 0.72 1.87E−02 11 35LYD482 0.82 3.41E−03 11 34 LYD482 0.74 1.47E−02 11 31 LYD483 0.772.42E−02 2 12 LYD483 0.74 3.73E−02 2 11 LYD483 0.75 1.95E−02 3 3 LYD4830.83 2.98E−03 8 46 LYD484 0.73 1.63E−02 1 22 LYD484 0.75 1.95E−02 2 3LYD484 0.81 8.10E−03 2 1 LYD487 0.78 2.17E−02 2 12 LYD487 0.74 2.39E−022 3 LYD487 0.75 1.99E−02 2 1 LYD487 0.84 9.32E−03 2 11 LYD489 0.722.72E−02 3 3 LYD489 0.90 2.63E−03 2 12 LYD489 0.81 1.44E−02 2 11 LYD4890.81 4.72E−03 11 42 LYD489 0.83 3.14E−03 11 38 LYD491 0.70 5.16E−02 2 12LYD491 0.74 3.46E−02 2 11 LYD491 0.74 2.24E−02 3 3 LYD491 0.77 1.55E−023 1 LYD491 0.75 1.26E−02 9 35 LYD491 0.78 7.60E−03 9 34 LYD491 0.751.31E−02 9 31 LYD491 0.72 1.85E−02 11 34 LYD491 0.71 2.25E−02 11 31LYD492 0.83 3.20E−03 1 20 LYD492 0.73 1.67E−02 1 23 LYD492 0.71 2.06E−021 22 LYD492 0.76 1.07E−02 1 19 LYD492 0.83 5.13E−03 3 3 LYD492 0.801.04E−02 3 1 Table 16. Provided are the correlations (R) between theexpression levels yield improving genes and their homologs in varioustissues [Expression (Exp) sets] and the phenotypic performance [yield,biomass, growth rate and/or vigor components (Correlation vector (Corr.)ID)] under normal conditions across tomato ecotypes. P = p value.

Example 5 Production of B. juncea Transcriptom and High ThroughputCorrelation Analysis with Yield Parameters Using 60K B. junceaOligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis, the presentinventors utilized a B. juncea oligonucleotide micro-array, produced byAgilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot)chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=508791. Thearray oligonucleotide represents about 60,000 B. juncea genes andtranscripts. In order to define correlations between the levels of RNAexpression with yield components or vigor related parameters, variousplant characteristics of 11 different B. juncea varieties were analyzedand used for RNA expression analysis. The correlation between the RNAlevels and the characterized parameters was analyzed using Pearsoncorrelation test.

Correlation of B. juncea Genes' Expression Levels with PhenotypicCharacteristics Across Ecotype

Experimental Procedures

11 B. juncea varieties were grown in three repetitive plots, in field.Briefly, the growing protocol was as follows: B. juncea seeds were sownin soil and grown under normal condition till harvest. In order todefine correlations between the levels of RNA expression with yieldcomponents or vigor related parameters, the 11 different B. junceavarieties were analyzed and used for gene expression analyses.

TABLE 17 Tissues used for B, juncea transcriptom expression setsExpression Set Set ID Meristem at vegetative stage under normal growthconditions 1 Flower at flowering stage under normal growth conditions 2Leaf at vegetative stage under normal growth conditions 3 Pod (R1-R3)under normal growth conditions 4 Pod (R4-R5) under normal growthconditions 5 Provided are the identification (ID) digits of each of theB, juncea expression sets.

RNA extraction—All 11 selected B. juncea varieties were sample per eachtreatment. Plant tissues [leaf, Pod, Lateral meristem and flower]growing under normal conditions were sampled and RNA was extracted asdescribed above.

The collected data parameters were as follows:

Fresh weight (plot-harvest) [gr/plant]—total fresh weight per plot atharvest time normalized to the number of plants per plot.

Seed Weight [milligrams/plant]—total seeds from each plot was extracted,weighted and normalized for plant number in each plot.

Harvest index—The harvest index was calculated: seed weight/fresh weightDays till bolting/flowering—number of days till 50% bolting/floweringfor each plot.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed at time of flowering.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken for each plot.

Main branch—average node length—total length/total number of nods onmain branch.

Lateral branch—average node length—total length/total number of nods onlateral branch.

Main branch—20th length—the length of the pod on the 20^(th) node fromthe apex of main branch.

Lateral branch—20th length—the length of the pod on the 20^(th) nodefrom the apex of lateral branch.

Main branch—20th seed No.—number of seeds in the pod on the 20^(th) nodefrom the apex of main branch.

Lateral branch—20th seed number—number of seeds in the pod on the20^(th) node from the apex of lateral branch.

Number of lateral branches—total number of lateral branches, average ofthree plants per plot.

Main branch height [cm]—total length of main branch.

Min-lateral branch position—lowest node on the main branch that hasdeveloped lateral branch.

Max-lateral branch position [#node of main branch]—highest node on themain branch that has developed lateral branch.

Max-number of nodes in lateral branch—the highest number of node that alateral branch had per plant.

Max length of lateral branch [cm]—the highest length of lateral branchper plant.

Max diameter of lateral branch [mm]—the highest base diameter that alateral branch had per plant.

Oil Content—Indirect oil content analysis was carried out using NuclearMagnetic Resonance (NMR) Spectroscopy, which measures the resonanceenergy absorbed by hydrogen atoms in the liquid state of the sample [Seefor example, Conway T F. and Earle F R., 1963, Journal of the AmericanOil Chemists' Society; Springer Berlin/Heidelberg, ISSN: 0003-021X(Print) 1558-9331 (Online)];

Fresh weight (single plant) (gr/plant)—average fresh weight of threeplants per plot taken at the middle of the season.

Main branch base diameter [mm]—the based diameter of main branch,average of three plants per plot.

1000 Seeds[gr]—weight of 1000 seeds per plot.

Experimental Results

Eleven different B. juncea varieties (i.e., Lines 1-11) were grown andcharacterized for 23 parameters as specified in Table 18, below. Theaverage for each of the measured parameters was calculated using the JMPsoftware and values are summarized in Tables 19-20 below. Subsequentcorrelation analysis between the various transcriptom expression setsand the average parameters was conducted (Table 21). Results were thenintegrated to the database.

TABLE 18 Measured parameters in B, juncea accessions Correlatedparameter with Correlation ID Days till bolting (days) 1 Fresh weight(plot-harvest) [gr./plant] 2 Seed weight per plant (gr.) 3 Harvest index(ratio) 4 Days till flowering (days) 5 SPAD 6 Main branch-average nodelength (cm) 7 Lateral branch-average node length (cm) 8 Main branch-20thlength (cm) 9 Lateral branch-20th length (cm) 10 Main branch-20th seednumber (number) 11 Lateral branch-20th seed number (number) 12 Number oflateral branches (number) 13 Main branch height [cm] 14 Min-Lateralbranch position ([No. of node of main branch) 15 Max-Lateral branchosition [No. of node of main branch] 16 Max-Number of nodes in lateralbranch (number) 17 Max-Length of lateral branch [cm] 18 Max-Diameter oflateral branch [mm] 19 Oil content (mg) 20 Fresh weight (single plant)[gr./plant] 21 Main branch base diameter [mm] 22 1000 Seeds [gr.] 23Provided are the B, juncea correlated parameters. “gr.” = grams; mm =millimeters; “cm” = centimeters; “mg” = milligrams; “SPAD” = chlorophylllevels;

TABLE 19 Measured parameters in B. juncea accessions (lines 1-6)Ecotype/ Correlation ID No. Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 157.33 60.33 59.67 56.33 55.00 46.67 2 69.24 45.22 39.27 49.11 43.9546.42 3 0.00 0.01 0.01 0.01 0.01 0.01 4 0.00 0.00 0.00 0.00 0.00 0.00 566.00 69.67 69.33 66.00 61.33 53.00 6 33.02 30.01 32.83 37.53 41.4435.41 7 0.48 0.41 0.63 0.43 0.38 0.68 8 0.65 0.43 0.74 0.57 0.56 0.79 94.28 3.72 3.62 3.50 2.74 5.20 10 4.32 3.69 4.14 3.37 3.06 3.96 11 13.2213.67 10.44 14.11 9.78 15.22 12 13.00 14.00 13.22 13.44 11.00 13.11 1315.22 14.89 13.56 14.89 14.00 9.78 14 140.72 125.22 112.44 133.39 142.00101.50 15 6.78 6.33 5.56 3.67 3.00 3.11 16 15.22 14.89 13.56 14.89 14.0010.89 17 5.22 7.00 5.22 7.00 6.56 9.44 18 40.44 47.22 41.61 60.50 59.7859.44 19 4.20 4.85 4.34 5.74 5.87 5.68 20 40.19 40.71 40.91 38.57 40.1442.63 21 197.78 142.22 147.22 243.33 192.33 163.78 22 14.53 11.99 19.9114.32 12.59 12.30 23 3.76 2.21 3.26 2.36 2.00 3.12 Table 19: Providedare the values of each of the parameters (as described above) measuredin B. juncea accessions (line numbers) under normal conditions.

TABLE 20 Measured parameters in B. juncea accessions (lines 7-11)Ecotype/Correlation ID No. Line-7 Line-8 Line-9 Line-10 Line-11 1 59.0054.33 59.67 57.33 53.00 2 36.14 32.58 33.16 63.23 60.94 3 0.00 0.00 0.000.01 0.01 4 0.00 0.00 0.00 0.00 0.00 5 69.67 63.67 69.67 71.00 58.33 633.17 32.87 34.80 31.82 41.49 7 0.40 0.63 0.57 0.59 1.55 8 0.57 0.760.96 0.78 0.90 9 3.91 3.98 3.46 3.73 4.04 10 4.33 4.21 4.14 4.04 3.88 1112.00 12.67 9.89 11.56 15.56 12 11.89 13.44 11.22 13.22 14.00 13 16.4414.33 14.56 14.11 16.78 14 145.39 131.56 129.89 131.56 116.44 15 7.786.22 5.56 4.89 5.33 16 16.44 14.33 14.56 14.11 16.78 17 6.11 5.22 5.676.56 6.00 18 47.28 47.33 44.67 58.67 47.17 19 4.52 4.89 4.68 5.56 5.4920 41.34 40.82 40.82 38.14 37.21 21 164.44 181.11 176.22 217.89 261.1122 12.60 12.91 12.56 13.77 13.56 23 3.34 3.09 3.39 3.40 2.39 Providedare the values of each of the parameters (as described above) measuredin B. juncea accessions (line numbers) under normal conditions.

TABLE 21 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across B. Juncea accessions Corr.Gene Exp. Corr. Gene Exp. Set Name R P value set Set ID Name R P valueset ID LYD346 0.76 6.81E−03 5 20 LYD347 0.84 3.86E−02 2 3 LYD347 0.777.40E−02 2 2 LYD347 0.85 3.34E−02 2 12 LYD348 0.70 1.18E−01 2 19 LYD3480.78 6.45E−02 2 11 LYD348 0.96 2.23E−03 2 21 LYD348 0.89 1.78E−02 2 3LYD348 0.79 6.14E−02 2 7 LYD348 0.94 6.04E−03 2 2 LYD348 0.77 5.36E−03 517 LYD349 0.95 8.71E−05 1 21 LYD349 0.79 6.32E−02 2 21 LYD349 0.971.06E−03 2 3 LYD349 0.77 7.19E−02 2 7 LYD349 0.85 3.18E−02 2 2 LYD3490.74 9.30E−02 2 12 LYD349 0.70 2.40E−02 3 22 LYD349 0.84 1.32E−03 5 8LYD351 0.86 2.81E−03 1 2 LYD351 0.70 1.20E−01 2 21 LYD351 0.91 1.08E−022 3 LYD351 0.92 9.53E−03 2 2 LYD351 0.84 3.73E−02 2 12 LYD351 0.731.02E−02 5 7 LYD351 0.71 1.50E−02 5 8 LYD352 0.78 1.24E−02 1 6 LYD3520.83 5.97E−03 1 21 LYD352 0.78 1.30E−02 1 4 LYD352 0.73 2.45E−02 1 3LYD352 0.90 1.11E−03 1 7 LYD352 0.72 1.05E−01 2 20 LYD352 0.85 3.11E−022 4 LYD353 0.93 3.25E−04 1 11 LYD353 0.71 3.22E−02 1 17 LYD353 0.882.07E−02 2 11 LYD353 0.80 5.37E−02 2 21 LYD353 0.84 3.75E−02 2 3 LYD3530.97 1.03E−03 2 7 LYD354 0.94 4.59E−03 2 3 LYD354 0.72 1.05E−01 2 2LYD354 0.77 7.17E−02 2 12 LYD354 0.77 1.59E−02 1 17 LYD354 0.74 2.15E−021 9 LYD354 0.71 1.39E−02 5 20 LYD354 0.72 1.20E−02 5 9 LYD355 0.853.49E−03 1 11 LYD355 0.90 8.14E−04 1 9 LYD355 0.87 2.61E−02 2 21 LYD3550.95 3.74E−03 2 3 LYD355 0.72 1.07E−01 2 7 LYD355 0.94 5.40E−03 2 2LYD355 0.79 4.05E−03 5 8 LYD356 0.73 1.68E−02 3 10 LYD356 0.79 7.12E−033 23 LYD357 0.92 8.69E−03 2 11 LYD357 0.87 2.54E−02 2 21 LYD357 0.882.07E−02 2 3 LYD357 0.98 5.08E−04 2 7 LYD357 0.73 1.02E−01 2 12 LYD3570.82 3.51E−03 3 4 LYD358 0.86 2.81E−03 1 4 LYD358 0.78 6.49E−02 2 20LYD358 0.86 2.77E−02 2 4 LYD358 0.88 7.61E−04 3 6 LYD358 0.72 1.29E−02 53 LYD359 0.80 5.55E−02 2 6 LYD359 0.78 6.68E−02 2 11 LYD359 0.853.12E−02 2 21 LYD359 0.94 5.89E−03 2 3 LYD359 0.90 1.34E−02 2 7 LYD3590.79 6.11E−03 3 6 LYD360 0.76 1.86E−02 1 4 LYD360 0.70 1.21E−01 2 10LYD360 0.77 7.03E−02 2 1 LYD360 0.89 1.89E−02 2 23 LYD360 0.82 4.39E−022 5 LYD360 0.91 1.14E−02 2 8 LYD360 0.70 1.62E−02 5 4 LYD361 0.911.23E−02 2 4 LYD361 0.82 3.94E−03 3 7 LYD361 0.85 1.84E−03 3 8 LYD3610.76 6.39E−03 5 22 LYD362 0.82 7.41E−03 1 6 LYD362 0.82 6.74E−03 1 7LYD362 0.78 6.84E−02 2 4 LYD362 0.72 2.00E−02 3 2 LYD364 0.75 1.97E−02 123 LYD364 0.77 7.31E−02 2 21 LYD364 0.92 9.20E−03 2 3 LYD364 0.891.74E−02 2 2 LYD364 0.72 1.05E−01 2 12 LYD365 0.86 2.66E−02 2 11 LYD3650.83 3.98E−02 2 9 LYD365 0.84 3.55E−02 2 16 LYD365 0.84 3.55E−02 2 13LYD366 0.89 1.67E−02 2 11 LYD366 0.90 1.55E−02 2 21 LYD366 0.85 3.10E−022 3 LYD366 0.82 4.41E−02 2 7 LYD366 0.91 1.24E−02 2 2 LYD366 0.805.80E−02 2 12 LYD367 0.79 1.06E−02 1 7 LYD367 0.74 2.23E−02 1 8 LYD3670.88 1.92E−02 2 11 LYD367 0.71 1.10E−01 2 21 LYD367 0.80 5.61E−02 2 3LYD367 0.94 4.77E−03 2 7 LYD367 0.71 2.02E−02 3 6 LYD368 0.78 1.35E−02 14 LYD368 0.81 4.99E−02 2 6 LYD368 0.78 6.86E−02 2 21 LYD368 0.731.02E−01 2 3 LYD368 0.87 2.58E−02 2 7 LYD368 0.83 1.54E−03 5 23 LYD4970.81 7.77E−03 1 4 LYD497 0.89 1.60E−02 2 16 LYD497 0.89 1.60E−02 2 13LYD497 0.71 1.42E−02 5 18 LYD497 0.72 1.21E−02 5 17 LYD498 0.72 2.85E−021 7 LYD498 0.94 6.09E−03 2 11 LYD498 0.86 2.92E−02 2 7 LYD498 0.872.44E−02 2 16 LYD498 0.87 2.44E−02 2 13 LYD498 0.74 1.54E−02 3 19 LYD4980.78 7.69E−03 3 18 LYD499 0.71 1.12E−01 2 11 LYD499 0.94 4.67E−03 2 21LYD499 0.84 3.73E−02 2 3 LYD499 0.80 5.81E−02 2 7 LYD499 0.93 7.27E−03 22 LYD500 0.73 1.01E−01 2 20 LYD500 0.78 6.91E−02 2 4 LYD500 0.821.96E−03 5 20 LYD501 0.91 6.50E−04 1 7 LYD501 0.95 4.38E−03 2 11 LYD5010.84 3.49E−02 2 7 LYD501 0.84 3.77E−02 2 9 LYD501 0.91 1.21E−02 2 16LYD501 0.91 1.21E−02 2 13 LYD501 0.72 1.99E−02 3 21 Table 21. Providedare the correlations (R) between the expression levels of yieldimproving genes and their homologues in tissues [Leaves, meristem,flower and pods; Expression sets (Exp)] and the phenotypic performancein various yield, biomass, growth rate and/or vigor components[Correlation vector (corr.) ID] under normal conditions across B, junceaaccessions. P = p value.

Example 6 Production of B. juncea Transcriptom and High ThroughputCorrelation Analysis with Yield Parameters of Juncea Grown Under VariousPopulation Densities Using 60K B. juncea Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis, the presentinventors utilized a B. juncea oligonucleotide micro-array, produced byAgilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot)chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879]. Thearray oligonucleotide represents about 60,000 B. juncea genes andtranscripts. In order to define correlations between the levels of RNAexpression with yield components or vigor related parameters, variousplant characteristics of two different B. juncea varieties grown underseven different population densities were analyzed and used for RNAexpression analysis. The correlation between the RNA levels and thecharacterized parameters was analyzed using Pearson correlation test.

Correlation of B. juncea Genes' Expression Levels with PhenotypicCharacteristics Across Seven Population Densities for Two Ecotypes

Experimental Procedures

Two B. juncea varieties were grown in a field under seven populationdensities (10, 60, 120, 160, 200, 250 and 300 plants per m²) in tworepetitive plots. Briefly, the growing protocol was as follows: B.juncea seeds were sown in soil and grown under normal condition tillharvest. In order to define correlations between the levels of RNAexpression with yield components or vigor related parameters, the twodifferent B. juncea varieties grown under various population densitieswere analyzed and used for gene expression analyses. The correlationbetween the RNA levels and the characterized parameters was analyzedusing Pearson correlation test for each ecotype independently.

TABLE 22 Tissues used for B. juncea transcriptom expression setsExpression Set Set ID Meristem under normal growth conditions variouspopulation 1 + 2 densities Flower under normal growth conditions variouspopulation 3 densities Provided are the identification (ID) digits ofeach of the B, juncea expression sets.

RNA extraction—the two B. juncea varieties grown under seven populationdensities were sample per each treatment. Plant tissues [Flower andLateral meristem] growing under Normal conditions were sampled and RNAwas extracted as described above. For convenience, each micro-arrayexpression information tissue type has received a Set ID.

The collected data parameters were as follows:

Fresh weight (plot-harvest) [gr/plant]—total fresh weight per plot atharvest time normalized to the number of plants per plot.

Seed weight [gr/plant]—total seeds from each plot was extracted,weighted and normalized for plant number in each plot.

Harvest index—The harvest index was calculated: seed weight/fresh weight

Days till bolting/flowering—number of days till 50% bolting/floweringfor each plot.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed at time of flowering.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken for each plot.

Main branch—average node length—total length/total number of nods onmain branch.

Lateral branch—average node length—total length/total number of nods onlateral branch.

Main branch—20th length—the length of the pod on the 20^(th) node fromthe apex of main branch.

Lateral branch—20th length—the length of the pod on the 20^(th) nodefrom the apex of lateral branch.

Main branch—20th seed No.—number of seeds in the pod on the 20^(th) nodefrom the apex of main branch.

Lateral branch—20th seed number—number of seeds in the pod on the20^(th) node from the apex of lateral branch.

Number of lateral branches—total number of lateral branches, average ofthree plants per plot.

Main branch height [cm]—total length of main branch.

Min-Lateral branch position—lowest node on the main branch that hasdeveloped lateral branch.

Max-Lateral branch position [#node of main branch]—highest node on themain branch that has developed lateral branch.

Max-number of nodes in lateral branch—the highest number of node that alateral branch had per plant.

Max-length of lateral branch [cm]—the highest length of lateral branchper plant.

Max diameter of lateral branch [mm]—the highest base diameter that alateral branch had per plant.

Oil content—Indirect oil content analysis was carried out using NuclearMagnetic Resonance (NMR) Spectroscopy, which measures the resonanceenergy absorbed by hydrogen atoms in the liquid state of the sample [Seefor example, Conway T F. and Earle F R., 1963, Journal of the AmericanOil Chemists' Society; Springer Berlin/Heidelberg, ISSN: 0003-021X(Print) 1558-9331 (Online)];

Fresh weight (single plant) (gr/plant)—average fresh weight of threeplants per plot taken at the middle of the season.

Main branch base diameter [mm]—the based diameter of main branch,average of three plants per plot.

1000 Seeds [gr]—weight of 1000 seeds per plot.

Main branch-total number of pods—total number of pods on the mainbranch, average of three plants per plot.

Main branch-dist. 1-20—the length between the youngest pod and podnumber on the main branch, average of three plants per plot.

Lateral branch-total number of pods—total number of pods on the lowestlateral branch, average of three plants per plot.

Lateral branch-dis. 1-20—the length between the youngest pod and podnumber on the lowest lateral branch, average of three plants per plot.

Dry weight/plant—weight of total plants per plot at harvest after threedays at oven at 60° C. normalized for the number of plants per plot.

Total leaf area—Total leaf area per plot was calculated based on randomthree plants and normalized for number of plants per plot.

Total Perim.—total perimeter of leaves, was calculated based on randomthree plants and normalized for number of plants per plot.

Experimental Results

Two B. juncea varieties were grown under seven different populationdensities and characterized for 30 parameters as specified in Table 23below. The average for each of the measured parameter was calculatedusing the JMP software and values are summarized in Tables 24-26 below.Subsequent correlation analysis between the expression of selected genesin various transcriptom expression sets and the average parameters wasconducted. Results were then integrated to the database (Table 27).

TABLE 23 Correlation parameters in B, juncea accessions CorrelationCorrelated parameter with ID Main branch base diameter [mm] 1 FreshWeight (single plant) [gr./plant] 2 Main branch height [cm] 3 Number oflateral branches (number) 4 Min-Lateral branch position (number of 5node on the main stem) Max-Lateral branch position (number of 6 node onthe main stem) Max-Number of nodes in lateral branch (number) 7Max-Length of lateral branch [cm] 8 Max-Diameter of lateral branch [mm]9 Main branch-total number of pods (number) 10 Main branch-dist. 1-20 11Main branch-20th length (cm) 12 Main branch-20th seed number (number) 13Lateral branch-total number of pods (number) 14 Lateral branch-dist.1-20 15 Lateral branch-20th length (cm) 16 Lateral branch-20th seednumber (number) 17 Oil content (mg) 18 SPAD 19 days till bolting (days)20 days till flowering (days) 21 Fresh weight (at harvest)/plant(gr/plant) 22 Dry weight/plant (gr./plant) 23 Seed weight/plant(gr./plant) 24 Fresh weight (harvest)/hectare (Kg/hectare) 25 Dryweight/hectare (Kg./hectare) 26 Seed weight/hectare 27 1000Seeds [gr.]28 Total leaf area (cm) 29 Total perim (cm). 30 Provided are the B,juncea correlated parameters. “gr.” = grams; mm = millimeters; “cm” =centimeters; “mg” = milligrams; “SPAD” = chlorophyll levels; “Kg.” =kilograms;

TABLE 24 Measured parameters in B. juncea varieties at variouspopulation densities Variety at population density/ line 1- Correlationline 1-density: line 1-density: line 1- line 1- density: ID No. 10 120density: 160 density: 200 250 1 14.7666667 6.9 5.61666667 4.991666676.45 2 0.3675 0.03583333 0.03333333 0.02416667 0.0375 3 118.666667 115.5111.333333 106 117.5 4 17.1666667 19.1666667 15.8333333 19.333333318.333333 5 1 11 7 11 9 6 20 23 19 24 22 7 10 4 4 4 6 8 122 41 43 36 409 7.7 2.9 2.5 2 3.4 10 20 15.33333333 17.6666667 16.5 23.166667 11 42.3527.9 31.2166667 26.05 27.716667 12 5.11666667 4.633333333 4.6 4.666666674.7333333 13 20 17.66666667 18 18.5 17.666667 14 17.3333333 11.6666666710.6666667 10.1666667 12.5 15 40.7333333 17.53333333 19.0833333 15.6515.233333 16 5.11666667 4.483333333 4.36666667 4.33333333 4.35 1721.6666667 19.33333333 17 18.8333333 15.666667 18 28.855 29.615 29.5730.585 29.87 19 43.49 41.95 40.48 37.93 39.5 20 53 50.5 48 53 50 21 6764 64 64 64 22 0.25972617 0.017544463 0.01160373 0.00941177 0.0086383 230.07146015 0.007860795 0.00318829 0.00218658 0.0027891 24 0.020933780.001837079 0.00088821 0.00073613 0.0008761 25 22434.188 22067.2376332929.2929 18596.0411 20654.321 26 6109.01654 9857.366286 8940.697244363.21162 6702.2185 27 1797.45096 2307.336938 2552.83939 1466.273282100.3779 28 1.80123016 1.7524685 1.62082389 1.98973809 1.9222969 29508.273183 37.4855833 24.9985 14.33268 50.78652 30 862.832233 100.49826767.98265 37.90552 97.50658 Provided are the values of each of theparameters (as described in Table 23 above) measured in B. juncea 2varieties at the indicated population densities under normal conditions.For example, “line 1 density: 10” refers to Juncea variety 1 grown at apopulation density of 10 plants per m².

TABLE 25 Measured parameters in B. juncea varieties at variouspopulation densities Variety at population density/ line 1- line 1- line2- line 2- line 2- Correlation density: density: density: density:density: ID No. 300 60 10 120 160 1 3.95 7.3666667 18.9 7.80833336.79166667 2 0.02166667 0.074 0.335 0.0433333 0.03166667 3 108 116133.166667 144.58333 144.916667 4 17.8333333 16.166667 12.5 15.33333316.8333333 5 9 5 1 8 9 6 20 20 14 17 21 7 4 6 11 6 5 8 42 78 127 42 34 92.5 4.4 8.4 3 2.6 10 16.83333333 15.166667 30.66666667 35.16666729.83333333 11 31.85 37.583333 38.71666667 32.85 28.76666667 124.683333333 5.1 4.666666667 3.85 4.433333333 13 17.5 17.66666714.33333333 10.333333 13.83333333 14 9.833333333 14 29.8333333317.333333 12.83333333 15 17.73333333 28.25 33.41666667 14.2666679.833333333 16 4.4 4.95 4.483333333 3.6666667 3.983333333 17 17.1666666714.55 12.83333333 10.166667 12.33333333 18 25.215 26.775 34.39 38.6539.66 19 45.57 40.89 43.83 41.31 40.86 20 51.5 53 55 50.5 47 21 62.562.5 64 61 61 22 0.009480434 0.0470682 0.186308744 0.015699 0.01353018723 0.002374948 0.0111681 0.045443225 0.0045977 0.004239026 240.000755044 0.0031703 0.014292085 0.0015562 0.001265508 25 24019.7132633376.441 16427.35043 15747.619 18531.76931 26 6009.085327 7906.66283979.782952 4609.2529 5801.024836 27 1901.668907 2247.0135 1270.0392451560.5283 1732.849463 28 1.54010747 1.5648537 2.81538106 3.19543312.87691722 29 29.1283 76.394583 1338.57912 76.818567 34.4628 30 61.16926219.13607 1518.31188 162.79095 82.7731667 Provided are the values ofeach of the parameters (as described in Table 23 above) measured in B.juncea 2 varieties at the indicated population densities under normalconditions. For example, “line 2-density: 300” refers to Juncea variety2 grown at a population density of 300 plants per m².

TABLE 26 Measured parameters in B. juncea varieties at variouspopulation densities Variety at population line 2- line 2- line 2- line2- density/ density: density: density: density: Correlation ID No. 200250 300 60 1 6.95 7.533333 5.441667 8.766667 7 0.025 0.028333 0.0241670.065833 3 138.5 144.1667 135.75 157.3333 4 16.66667 16.66667 15.512.83333 5 8 10 8 3 6 18 19 18 16 7 4 6 4 11 8 23 38 25 109 9 2.1 2.82.35 8 10 30.83333 29.33333 25.33333 33.83333 11 25.3 26.38333 25.0666745.25 12 4.116667 4.116667 4.233333 4.433333 13 10.33333 11 10.6666713.16667 14 11.16667 13 9 18.5 15 8.6 10.98333 6.35 21.58333 16 4.0333333.966667 3.7 4.716667 17 10.66667 9.833333 9 11.16667 18 36.795 37.137.61 37.545 19 39.31 40.46 47.48 39.21 20 48 49 49 51.5 21 61 61 61 612/ 0.009797 0.008836 0.008388 0.039744 23 0.003773 0.002963 0.0025310.011524 24 0.000842 0.000819 0.000729 0.0034 25 17182.54 16833.3323055.66 20833.33 26 6581.384 5656.266 6882.516 6039.66 27 1472.1841560.8 2005.713 1780.966 28 3.256972 3.276912 3.430244 2.773618 2928.27737 41.3294 92.8963 218.1545 30 75.36597 83.49002 143.9019 328.9701Provided are the values of each of the parameters (as described in Table23 above) measured in B. juncea 2 varieties at the indicated populationdensities under normal conditions. For example, “line 2-density: 200”refers to Juncea variety 2 grown at a population density of 200 plantsper m².

TABLE 27 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions at different densities across B.Juncea accessions Exp. Corr. Set Exp. Corr. Set Gene Name R P value setID Gene Name R P value set ID LYD347 0.81 2.84E−02 2 13 LYD347 0.736.45E−02 2 21 LYD348 0.71 7.58E−02 2 26 LYD351 0.84 1.78E−02 2 6 LYD3510.76 4.93E−02 2 5 LYD351 0.80 3.02E−02 2 4 LYD352 0.89 6.74E−03 2 9LYD352 0.90 5.09E−03 2 8 LYD352 0.91 4.34E−03 2 1 LYD352 0.88 9.54E−03 27 LYD352 0.91 4.60E−03 2 15 LYD352 0.76 4.95E−02 2 16 LYD352 0.959.24E−04 2 24 LYD352 0.91 4.48E−03 2 13 LYD352 0.95 9.57E−04 2 29 LYD3520.83 2.19E−02 2 11 LYD352 0.96 6.22E−04 2 2 LYD352 0.82 2.37E−02 2 14LYD352 0.95 1.11E−03 2 23 LYD352 0.95 1.16E−03 2 30 LYD352 0.84 1.90E−022 21 LYD352 0.96 7.54E−04 2 22 LYD354 0.94 1.36E−03 2 9 LYD354 0.914.65E−03 2 8 LYD354 0.98 6.32E−05 2 1 LYD354 0.93 2.58E−03 2 7 LYD3540.80 3.11E−02 2 3 LYD354 0.88 8.26E−03 2 15 LYD354 0.88 8.18E−03 2 16LYD354 0.96 5.17E−04 2 24 LYD354 0.84 1.69E−02 2 12 LYD354 0.91 4.10E−032 13 LYD354 0.96 4.81E−04 2 29 LYD354 0.76 4.55E−02 2 11 LYD354 0.973.23E−04 2 2 LYD354 0.99 3.80E−05 2 14 LYD354 0.96 5.20E−04 2 23 LYD3540.96 6.03E−04 2 30 LYD354 0.92 3.42E−03 2 21 LYD354 0.96 6.14E−04 2 22LYD355 0.89 7.35E−03 2 5 LYD357 0.76 4.65E−02 2 9 LYD357 0.78 3.83E−02 28 LYD357 0.76 4.88E−02 2 7 LYD357 0.76 4.52E−02 2 15 LYD357 0.755.22E−02 2 24 LYD357 0.75 5.38E−02 2 12 LYD357 0.77 4.35E−02 2 29 LYD3570.83 2.20E−02 2 11 LYD357 0.75 5.01E−02 2 2 LYD357 0.74 5.71E−02 2 23LYD357 0.77 4.48E−02 2 30 LYD357 0.76 4.68E−02 2 22 LYD358 0.79 3.44E−022 9 LYD358 0.79 3.65E−02 2 8 LYD358 0.72 6.57E−02 2 1 LYD358 0.783.87E−02 2 7 LYD358 0.75 5.36E−02 2 3 LYD358 0.75 5.09E−02 2 15 LYD3580.87 1.05E−02 2 16 LYD358 0.93 2.62E−03 2 12 LYD358 0.88 8.16E−03 2 14LYD360 0.85 1.57E−02 2 9 LYD360 0.93 2.36E−03 2 8 LYD360 0.78 3.78E−02 21 LYD360 0.81 2.62E−02 2 7 LYD360 0.94 1.87E−03 2 15 LYD360 0.966.16E−04 2 16 LYD360 0.87 1.10E−02 2 24 LYD360 0.97 2.30E−04 2 12 LYD3600.79 3.33E−02 2 13 LYD360 0.86 1.29E−02 2 29 LYD360 0.95 8.96E−04 2 11LYD360 0.87 1.01E−02 2 2 LYD360 0.84 1.75E−02 2 14 LYD360 0.86 1.24E−022 23 LYD360 0.88 9.10E−03 2 30 LYD360 0.89 7.66E−03 2 22 LYD361 0.755.01E−02 2 13 LYD361 0.79 3.38E−02 2 21 LYD362 0.78 3.75E−02 2 9 LYD3620.75 5.21E−02 2 8 LYD362 0.86 1.28E−02 2 19 LYD362 0.84 1.70E−02 2 27LYD362 0.74 5.47E−02 2 1 LYD362 0.72 6.89E−02 2 7 LYD362 0.76 4.69E−02 215 LYD362 0.76 4.92E−02 2 24 LYD362 0.77 4.33E−02 2 29 LYD362 0.822.53E−02 2 11 LYD362 0.76 4.58E−02 2 2 LYD362 0.71 7.65E−02 2 14 LYD3620.76 4.79E−02 2 23 LYD362 0.77 4.16E−02 2 30 LYD362 0.76 4.95E−02 2 22LYD362 0.80 3.24E−02 2 26 LYD364 0.74 5.61E−02 2 6 LYD364 0.75 5.13E−022 28 LYD364 0.75 5.25E−02 2 4 LYD365 0.72 6.78E−02 2 18 LYD366 0.914.39E−03 2 5 LYD497 0.75 5.27E−02 2 5 LYD498 0.83 2.09E−02 2 5 LYD4990.76 4.79E−02 2 1 LYD499 0.78 3.69E−02 2 24 LYD499 0.85 1.42E−02 2 13LYD499 0.78 4.03E−02 2 29 LYD499 0.77 4.33E−02 2 2 LYD499 0.79 3.55E−022 23 LYD499 0.73 6.11E−02 2 30 LYD499 0.96 5.73E−04 2 21 LYD499 0.764.68E−02 2 22 LYD499 0.92 3.61E−03 2 17 LYD501 0.71 7.41E−02 2 15 LYD5010.85 1.56E−02 2 16 LYD501 0.82 2.45E−02 2 12 LYD501 0.76 4.65E−02 2 11LYD501 0.74 5.64E−02 2 5 Table 27. Provided are the correlations (R)between the expression levels of yield improving genes and theirhomologues in tissues [meristem and flower; Expression sets (Exp)] andthe phenotypic performance in various yield, biomass, growth rate and/orvigor components [Correlation vector (corr.) ID] under normal conditionsacross B, juncea accessions. P = p value.

Example 7 Production of Sorghum Transcriptom and High ThroughputCorrelation Analysis with ABST Related Parameters Using 44K SorghumOligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis between plantphenotype and gene expression level, the present inventors utilized asorghum oligonucleotide micro-array, produced by Agilent Technologies[Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent(dot) com/Scripts/PDS (dot) asp?lPage=50879]. The array oligonucleotiderepresents about 44,000 sorghum genes and transcripts. In order todefine correlations between the levels of RNA expression with ABST,yield and NUE components or vigor related parameters, various plantcharacteristics of 17 different sorghum hybrids were analyzed. Amongthem, 10 hybrids encompassing the observed variance were selected forRNA expression analysis. The correlation between the RNA levels and thecharacterized parameters was analyzed using Pearson correlation test[Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot)com/hyperstat/A34739 (dot) html].

Correlation of Sorghum Varieties Across Ecotypes Grown Under RegularGrowth Conditions, Severe Drought Conditions and Low Nitrogen Conditions

Experimental Procedures

17 Sorghum varieties were grown in 3 repetitive plots, in field.Briefly, the growing protocol was as follows:

1. Regular (normal) growth conditions: sorghum plants were grown in thefield using commercial fertilization and irrigation protocols (370 literper meter², fertilization of 14 units of 21% urea per entire growthperiod).

2. Drought conditions: sorghum seeds were sown in soil and grown undernormal condition until around 35 days from sowing, around stage V8(eight green leaves are fully expanded, booting not started yet). Atthis point, irrigation was stopped, and severe drought stress wasdeveloped.

3. Low Nitrogen fertilization conditions: sorghum plants were fertilizedwith 50% less amount of nitrogen in the field than the amount ofnitrogen applied in the regular growth treatment. All the fertilizer wasapplied before flowering.

Analyzed Sorghum tissues—All 10 selected Sorghum hybrids were sample pereach treatment. Tissues [Flag leaf, Flower meristem and Flower] fromplants growing under normal conditions, severe drought stress and lownitrogen conditions were sampled and RNA was extracted as describedabove. Each micro-array expression information tissue type has receiveda Set ID as summarized in Table 28 below.

TABLE 28 Sorghum transcriptom expression sets Expression Set Set ID Flagleaf at flowering stage under drought growth conditions 1 Flag leaf atflowering stage under low nitrogen 2 growth conditions Flag leaf atflowering stage under normal growth conditions 3 Flower meristem atflowering stage under drought 4 growth conditions Flower meristem atflowering stage under low 5 nitrogen growth conditions Flower meristemat flowering stage under normal 6 growth conditions Flower at floweringstage under drought growth conditions 7 Flower at flowering stage underlow nitrogen growth conditions 8 Flower at flowering stage under normalgrowth conditions 9 Provided are the sorghum transcriptom expressionsets 1-9. Flag leaf = the leaf below the flower; Flower meristem =Apical meristem following panicle initiation; Flower = the flower at theanthesis day. Expression sets 1, 4 and 7 are from plants grown underdrought conditions; Expresion sets 2, 5 and 8 are from plants grownunder low nitrogen conditions; Expression sets 3, 6 and 9 are fromplants grown under normal conditions.

The following parameters were collected using digital imaging system:

At the end of the growing period the grains were separated from thePlant ‘Head’ and the following parameters were measured and collected:

Average Grain Area (cm²)—A sample of ˜200 grains were weight,photographed and images were processed using the below described imageprocessing system. The grain area was measured from those images and wasdivided by the number of grains.

(I) Upper and Lower Ratio Average of Grain Area, width, diameter andperimeter—Grain projection of area, width, diameter and perimeter wereextracted from the digital images using open source package imagej(nih). Seed data was analyzed in plot average levels as follows:

Average of all seeds.

Average of upper 20% fraction—contained upper 20% fraction of seeds.

Average of lower 20% fraction—contained lower 20% fraction of seeds.

Further on, ratio between each fraction and the plot average wascalculated for each of the data parameters.

At the end of the growing period 5 ‘Heads’ were, photographed and imageswere processed using the below described image processing system.

(II) Head Average Area (cm²)—At the end of the growing period 5 ‘Heads’were, photographed and images were processed using the below describedimage processing system. The ‘Head’ area was measured from those imagesand was divided by the number of ‘Heads’.

(III) Head Average Length (cm)—At the end of the growing period 5‘Heads’ were, photographed and images were processed using the belowdescribed image processing system. The ‘Head’ length (longest axis) wasmeasured from those images and was divided by the number of ‘Heads’.

(IV) Head Average width (cm)—At the end of the growing period 5 ‘Heads’were, photographed and images were processed using the below describedimage processing system. The ‘Head’ width was measured from those imagesand was divided by the number of ‘Heads’.

(V) Head Average width (cm)—At the end of the growing period 5 ‘Heads’were, photographed and images were processed using the below describedimage processing system. The ‘Head’ perimeter was measured from thoseimages and was divided by the number of ‘Heads’.

The image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37, Java based image processing software, which wasdeveloped at the U.S. National Institutes of Health and is freelyavailable on the internet at Hypertext Transfer Protocol://rsbweb (dot)nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels(3888×2592 pixels) and stored in a low compression JPEG (JointPhotographic Experts Group standard) format. Next, image processingoutput data for seed area and seed length was saved to text files andanalyzed using the JMP statistical analysis software (SAS institute).

Additional parameters were collected either by sampling 5 plants perplot or by measuring the parameter across all the plants within theplot.

Total Grain Weight/Head (gr.) (grain yield)—At the end of the experiment(plant ‘Heads’) heads from plots within blocks A-C were collected. 5heads were separately threshed and grains were weighted, all additionalheads were threshed together and weighted as well. The average grainweight per head was calculated by dividing the total grain weight bynumber of total heads per plot (based on plot). In case of 5 heads, thetotal grains weight of 5 heads was divided by 5.

FW Head/Plant gram—At the end of the experiment (when heads wereharvested) total and 5 selected heads per plots within blocks A-C werecollected separately. The heads (total and 5) were weighted (gr.)separately and the average fresh weight per plant was calculated fortotal (FW Head/Plant gr. based on plot) and for 5 (FW Head/Plant gr.based on 5 plants).

Plant height—Plants were characterized for height during growing periodat 5 time points. In each measure, plants were measured for their heightusing a measuring tape. Height was measured from ground level to top ofthe longest leaf.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed 64 days post sowing.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken per plot.

Vegetative fresh weight and Heads—At the end of the experiment (whenInflorescence were dry) all Inflorescence and vegetative material fromplots within blocks A-C were collected. The biomass and Heads weight ofeach plot was separated, measured and divided by the number of Heads.

Plant biomass (Fresh weight)—At the end of the experiment (whenInflorescence were dry) the vegetative material from plots within blocksA-C were collected. The plants biomass without the Inflorescence weremeasured and divided by the number of Plants.

FW Heads/(FW Heads+FW Plant)—The total fresh weight of heads and theirrespective plant biomass were measured at the harvest day. The headsweight was divided by the sum of weights of heads and plants.

Experimental Results

17 different sorghum varieties were grown and characterized fordifferent parameters (Table 29). The average for each of the measuredparameter was calculated using the JMP software (Tables 30-31) and asubsequent correlation analysis between the various transcriptom sets(Table 28) and the average parameters (Tables 30-31) was conductedResults were then integrated to the database (Table 32).

TABLE 29 Sorghum correlated parameters (vectors) Correlated parameterwith Correlation ID Total grain weight/Head gr (based on plot), Normal 1Total grain weight/Head gr (based on 5 heads), Normal 2 Head AverageArea (cm²), Normal 3 Head Average Perimeter (cm), Normal 4 Head AverageLength (cm), Normal 5 Head Average Width (cm), Normal 6 Average GrainArea (cm²), Normal 7 Upper Ratio Average Grain Area, Normal 8 LowerRatio Average Grain Area, Normal 9 Lower Ratio Average Grain Perimeter,Normal 10 Lower Ratio Average Grain Length, Normal 11 Lower RatioAverage Grain Width, Normal 12 Final Plant Height (cm), Normal 13FW-Head/Plant gr (based on 5 plants), Normal 14 FW-Head/Plant gr (basedon plot), Normal 15 FW/Plant gr (based on plot), Normal 16 Leaf SPAD 64DPS (Days Post Sowing), Normal 17 FW Heads/(FW Heads + FW Plants)(allplot), Normal 18 [Plant biomass (FW)/SPAD 64 DPS], Normal 19 [GrainYield + plant biomass/SPAD 64 DPS], Normal 20 [Grain yield/SPAD 64 DPS],Normal 21 Total grain weight/Head (based on plot) gr., Low N 22 Totalgrain weight/Head gr (based on 5 heads), Low N 23 Head Average Area(cm²), Low N 24 Head Average Perimeter (cm), Low N 25 Head AverageLength (cm), Low N 26 Head Average Width (cm), Low N 27 Average GrainArea (cm²), Low N 28 Upper Ratio Average Grain Area, Low N 29 LowerRatio Average Grain Area, Low N 30 Lower Ratio Average Grain Perimeter,Low N 31 Lower Ratio Average Grain Length, Low N 32 Lower Ratio AverageGrain Width, Low N 33 Final Plant Height (cm), Low N 34 FW-Head/Plantgr. (based on 5 plants), Low N 35 FW-Head/Plant gr. (based on plot), LowN 36 FW/Plant gr. (based on plot), Low N 37 Leaf SPAD 64 DPS (Days PostSowing), Low N 38 FW Heads/(FW Heads + FW Plants)(all plot), Low N 39[Plant biomass (FW)/SPAD 64 DPS], Low N 40 [Grain Yield + plantbiomass/SPAD 64 DPS], Low N 41 [Grain yield/SPAD 64 DPS], Low N 42 Totalgrain weight/Head gr,(based on plot) Drought 43 Head Average Area (cm²),Drought 44 Head Average Perimeter (cm), Drought 45 Head Average Length(cm), Drought 46 Head Average Width (cm), Drought 47 Average Grain Area(cm²), Drought 48 Upper Ratio Average Grain Area, Drought 49 Final PlantHeight (cm), Drought 50 FW-Head/Plant gr. (based on plot), Drought 51FW/Plant gr (based on plot), Drought 52 Leaf SPAD 64 DPS (Days PostSowing), Drought 53 FW Heads/(FW Heads + FW Plants)(all plot), Drought54 [Plant biomass (FW)/SPAD 64 DPS], Drought 55 Provided are the Sorghumcorrelated parameters (vectors). “gr.” = grams; “SPAD” = chlorophylllevels; “FW” = Plant Fresh weight; “normal” = standard growthconditions.

TABLE 30 Measured parameters in Sorghum accessions (Lines 1-9) Ecotype/Correlation ID No. Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7Line-8 Line-9 1 31.12 26.35 18.72 38.38 26.67 28.84 47.67 31.00 39.99 247.40 46.30 28.37 70.40 32.15 49.23 63.45 44.45 56.65 3 120.14 167.6085.14 157.26 104.00 102.48 168.54 109.32 135.13 4 61.22 67.90 56.2665.38 67.46 67.46 74.35 56.16 61.64 5 25.58 26.84 21.02 26.84 23.1421.82 31.33 23.18 25.70 6 5.97 7.92 4.87 7.43 5.58 5.88 6.78 5.99 6.62 70.10 0.11 0.13 0.13 0.14 0.14 0.11 0.11 0.10 8 1.22 1.30 1.13 1.14 1.161.15 1.19 1.23 1.25 9 0.83 0.74 0.78 0.80 0.70 0.70 0.83 0.81 0.84 100.91 0.87 0.91 0.95 0.90 0.91 0.91 0.91 0.92 11 0.91 0.88 0.92 0.91 0.890.88 0.91 0.90 0.92 12 0.91 0.83 0.85 0.87 0.79 0.80 0.90 0.89 0.91 1395.25 79.20 197.85 234.20 189.40 194.67 117.25 92.80 112.65 14 406.50518.00 148.00 423.00 92.00 101.33 423.50 386.50 409.50 15 175.15 223.4956.40 111.62 67.34 66.90 126.18 107.74 123.86 16 162.56 212.59 334.83313.46 462.28 318.26 151.13 137.60 167.98 17 43.01 43.26 44.74 45.7641.61 45.21 45.14 43.03 18 0.51 0.51 0.12 0.26 0.12 0.18 0.46 0.43 0.4219 0.72 0.43 0.86 0.58 0.69 1.05 0.69 0.93 0.84 20 4.50 8.17 7.87 10.688.34 4.40 3.74 4.83 3.67 21 3.78 7.74 7.01 10.10 7.65 3.34 3.05 3.902.83 22 25.95 30.57 19.37 35.62 25.18 22.18 49.96 27.48 51.12 23 50.2750.93 36.13 73.10 37.87 36.40 71.67 35.00 76.73 24 96.24 214.72 98.59182.83 119.64 110.19 172.36 84.81 156.25 25 56.32 79.20 53.25 76.2167.27 59.49 79.28 51.52 69.88 26 23.22 25.58 20.93 28.43 24.32 22.6332.11 20.38 26.69 27 5.26 10.41 5.93 8.25 6.19 6.12 6.80 5.25 7.52 280.11 0.11 0.14 0.12 0.14 0.13 0.12 0.12 0.12 29 1.18 1.31 1.11 1.21 1.191.18 1.16 1.23 1.17 30 0.82 0.77 0.81 0.79 0.78 0.80 0.83 0.79 0.81 310.90 0.88 0.92 0.90 0.92 0.92 0.92 0.89 0.90 32 0.91 0.90 0.92 0.90 0.910.93 0.92 0.89 0.90 33 0.90 0.85 0.89 0.88 0.86 0.87 0.91 0.89 0.90 34104.00 80.93 204.73 125.40 225.40 208.07 121.40 100.27 121.13 35 388.00428.67 297.67 280.00 208.33 303.67 436.00 376.33 474.67 36 214.78 205.0573.49 122.96 153.07 93.23 134.11 77.43 129.63 37 204.78 199.64 340.51240.60 537.78 359.40 149.20 129.06 178.71 38 38.33 38.98 42.33 40.9043.15 39.85 42.68 43.31 39.01 39 0.51 0.51 0.17 0.39 0.21 0.19 0.48 0.370.42 40 5.34 5.12 8.05 5.88 12.46 9.02 3.50 2.98 4.58 41 6.02 5.91 8.506.75 13.05 9.58 4.67 3.61 5.89 42 0.68 0.78 0.46 0.87 0.58 0.56 1.170.63 1.31 43 22.11 16.77 9.19 104.44 3.24 22.00 9.97 18.58 29.27 4483.14 107.79 88.68 135.91 90.76 123.95 86.06 85.20 113.10 45 52.78 64.4956.59 64.37 53.21 71.66 55.61 52.96 69.83 46 21.63 21.94 21.57 22.0120.99 28.60 21.35 20.81 24.68 47 4.83 6.31 5.16 7.78 5.28 5.49 5.04 5.075.77 48 0.10 0.11 0.11 0.09 0.09 0.11 49 1.31 1.19 1.29 1.46 1.21 1.2150 89.40 75.73 92.10 94.30 150.80 110.73 99.20 84.00 99.00 51 154.90122.02 130.51 241.11 69.03 186.41 62.11 39.02 58.94 52 207.99 138.02255.41 402.22 233.55 391.75 89.31 50.61 87.02 53 40.58 40.88 45.01 42.3045.24 40.56 44.80 45.07 40.65 54 0.42 0.47 0.42 0.37 0.23 0.31 0.41 0.440.40 55 5.13 3.38 5.67 9.51 5.16 9.66 1.99 1.12 2.14 Table 30: Providedare the values of each of the parameters (as described in Table 29above) measured in Sorghum accessions (ecotype) under normal, lownitrogen and drought conditions. Growth conditions are specified in theexperimental procedure section.

TABLE 31 Additional measured parameters in Sorghum accessions (Lines10-17) Ecotype/ Correlation ID No. Line-10 Line-11 Line-12 Line-13Line-14 Line-15 Line-16 Line-17 1 38.36 32.10 32.69 32.79 51.53 35.7138.31 42.44 2 60.00 45.45 58.19 70.60 70.10 53.95 59.87 52.65 3 169.03156.10 112.14 154.74 171.70 168.51 162.51 170.46 4 71.40 68.56 56.4467.79 71.54 78.94 67.03 74.11 5 28.82 28.13 22.97 28.09 30.00 30.5427.17 29.26 6 7.42 6.98 6.19 7.02 7.18 7.00 7.39 7.35 7 0.12 0.12 0.110.12 0.11 0.10 0.11 0.11 8 1.24 1.32 1.22 1.18 1.18 1.22 1.25 1.22 90.79 0.77 0.80 0.81 0.82 0.81 0.82 0.82 10 0.93 0.91 0.92 0.90 0.91 0.900.91 0.91 11 0.92 0.89 0.91 0.91 0.91 0.90 0.90 0.91 12 0.85 0.86 0.880.90 0.90 0.91 0.90 0.90 13 97.50 98.00 100.00 105.60 151.15 117.10124.45 126.50 14 328.95 391.00 435.75 429.50 441.00 415.75 429.50 428.5015 102.75 82.33 77.59 91.17 150.44 109.10 107.58 130.88 16 128.97 97.6299.32 112.24 157.42 130.55 135.66 209.21 17 45.59 44.83 45.33 46.5443.99 45.09 45.14 43.13 18 0.44 0.46 0.45 0.45 0.51 0.46 0.44 0.39 190.72 0.72 0.70 1.17 0.79 0.85 0.98 20 2.89 2.91 3.12 4.75 3.69 3.85 5.8421 2.18 2.19 2.41 3.58 2.90 3.01 4.85 22 36.84 29.45 26.70 29.42 51.1237.04 39.85 41.78 23 57.58 42.93 36.47 68.60 71.80 49.27 43.87 52.07 24136.71 137.70 96.54 158.19 163.95 138.39 135.46 165.64 25 66.17 67.3757.90 70.61 73.76 66.87 65.40 75.97 26 26.31 25.43 23.11 27.87 28.8827.64 25.52 30.33 27 6.59 6.85 5.32 7.25 7.19 6.27 6.57 6.82 28 0.130.13 0.12 0.12 0.11 0.11 0.12 0.11 29 1.22 1.24 1.19 1.23 1.16 1.34 1.211.21 30 0.77 0.74 0.80 0.79 0.82 0.80 0.81 0.81 31 0.91 0.89 0.90 0.900.91 0.89 0.90 0.90 32 0.91 0.89 0.90 0.89 0.91 0.89 0.89 0.90 33 0.860.84 0.90 0.89 0.91 0.90 0.90 0.90 34 94.53 110.00 115.07 104.73 173.67115.60 138.80 144.40 35 437.67 383.00 375.00 425.00 434.00 408.67 378.50432.00 36 99.83 76.95 84.25 92.24 138.83 113.32 95.50 129.49 37 124.27101.33 132.12 117.90 176.99 143.67 126.98 180.45 38 42.71 40.08 43.9845.44 44.75 42.58 43.81 46.73 39 0.44 0.43 0.39 0.44 0.44 0.44 0.43 0.4240 2.91 2.53 3.00 2.60 3.96 3.38 2.90 3.86 41 3.77 3.26 3.61 3.24 5.104.25 3.81 4.76 42 0.86 0.73 0.61 0.65 1.14 0.87 0.91 0.89 43 10.45 14.7712.86 18.24 11.60 18.65 16.36 44 100.79 80.41 126.89 86.41 92.29 77.8976.93 45 65.14 55.27 69.06 53.32 56.29 49.12 51.88 46 24.28 21.95 24.9819.49 20.42 16.81 18.88 47 5.37 4.66 6.35 5.58 5.76 5.86 5.10 50 92.2081.93 98.80 86.47 99.60 83.00 83.53 92.30 51 76.37 33.47 42.20 41.53131.67 60.84 44.33 185.44 52 120.43 37.21 48.18 44.20 231.60 116.01123.08 342.50 53 45.43 42.58 44.18 44.60 42.41 43.25 40.30 40.75 54 0.440.47 0.47 0.48 0.35 0.35 0.23 0.33 55 2.65 0.87 1.09 0.99 5.46 2.68 3.058.40 Table 31: Provided are the values of each of the parameters (asdescribed above) measured in Sorghum accessions (ecotype) under normal,low nitrogen and drought conditions. Growth conditions are specified inthe experimental procedure section.

TABLE 32 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal or abiotic stress conditions across Sorghumaccessions Exp. Corr. Set Exp. Corr. Set Gene Name R P value set ID GeneName R P value set ID LYD423 0.77 8.63E−03 6 13 LYD423 0.72 1.85E−02 615 LYD423 0.80 5.31E−03 6 16 LYD423 0.81 4.12E−03 6 1 LYD423 0.946.58E−05 2 29 LYD423 0.84 2.13E−03 4 55 LYD423 0.70 2.37E−02 4 51 LYD4230.84 2.18E−03 4 52 LYD423 0.91 2.94E−04 5 36 LYD423 0.73 1.72E−02 5 30LYD423 0.86 1.23E−03 5 41 LYD423 0.91 2.82E−04 5 40 LYD423 0.71 2.20E−025 39 LYD423 0.85 2.08E−03 5 32 LYD423 0.89 5.04E−04 5 37 LYD423 0.761.15E−02 3 7 LYD423 0.72 2.95E−02 7 44 LYD423 0.76 1.81E−02 7 47 LYD4240.86 1.41E−03 6 13 LYD424 0.72 1.87E−02 6 1 LYD424 0.83 2.76E−03 4 55LYD424 0.80 5.92E−03 4 51 LYD424 0.84 2.20E−03 4 52 LYD425 0.82 3.55E−036 13 LYD425 0.84 2.37E−03 6 1 LYD425 0.73 1.58E−02 5 35 LYD425 0.712.25E−02 5 22 LYD425 0.85 1.74E−03 1 55 LYD425 0.72 1.95E−02 1 51 LYD4250.86 1.32E−03 1 52 LYD427 0.77 9.39E−03 6 13 LYD427 0.87 1.03E−03 6 1LYD427 0.73 1.75E−02 6 2 LYD427 0.71 2.11E−02 6 11 LYD427 0.89 4.79E−049 2 LYD427 0.82 4.05E−03 4 55 LYD427 0.72 1.87E−02 4 51 LYD427 0.823.41E−03 4 52 LYD427 0.71 2.16E−02 5 30 LYD427 0.73 1.58E−02 5 37 LYD4270.81 4.42E−03 3 2 LYD427 0.71 2.05E−02 1 50 LYD428 0.73 1.59E−02 2 34LYD431 0.74 1.42E−02 6 13 LYD431 0.87 9.18E−04 4 55 LYD431 0.72 1.85E−024 51 LYD431 0.86 1.24E−03 4 52 LYD432 0.71 2.07E−02 6 8 LYD432 0.702.31E−02 6 7 LYD432 0.79 6.56E−03 2 34 LYD432 0.83 3.06E−03 8 28 LYD4320.72 1.85E−02 3 2 LYD432 0.73 1.69E−02 1 53 LYD433 0.73 1.60E−02 6 5LYD433 0.81 4.12E−03 6 2 LYD433 0.70 3.45E−02 4 44 LYD433 0.70 2.39E−025 30 LYD434 0.73 1.56E−02 6 13 LYD434 0.74 1.35E−02 4 55 LYD434 0.796.92E−03 4 51 LYD434 0.75 1.29E−02 4 52 LYD434 0.91 7.59E−04 7 44 LYD4340.81 7.61E−03 7 47 LYD434 0.91 6.53E−04 7 45 LYD434 0.72 2.77E−02 7 46LYD435 0.76 9.94E−03 6 7 LYD435 0.72 1.97E−02 9 1 LYD436 0.85 1.95E−03 613 LYD436 0.77 9.58E−03 6 1 LYD436 0.92 1.39E−04 4 55 LYD436 0.842.39E−03 4 51 LYD436 0.93 1.13E−04 4 52 LYD436 0.77 9.25E−03 8 28 LYD4360.75 1.17E−02 5 37 LYD507 0.71 2.17E−02 9 1 LYD507 0.77 8.97E−03 8 32LYD507 0.74 1.54E−02 8 31 LYD508 0.76 1.03E−02 6 1 LYD508 0.75 1.16E−024 55 LYD508 0.77 9.61E−03 4 52 LYD508 0.77 8.64E−03 5 22 LYD508 0.712.11E−02 5 42 LYD508 0.73 1.72E−02 3 16 LYD509 0.81 4.73E−03 6 8 LYD5090.71 2.16E−02 9 13 LYD509 0.80 4.97E−03 9 1 LYD509 0.74 2.22E−02 7 44LYD509 0.78 1.38E−02 7 47 LYD509 0.71 3.30E−02 1 44 LYD509 0.70 3.41E−021 45 LYD509 0.81 7.56E−03 1 46 LYD510 0.79 6.74E−03 6 13 LYD510 0.731.76E−02 6 18 LYD510 0.71 2.21E−02 6 4 LYD510 0.73 1.68E−02 6 5 LYD5100.75 1.17E−02 6 1 LYD510 0.87 1.03E−03 4 55 LYD510 0.75 1.33E−02 4 51LYD510 0.87 9.50E−04 4 52 LYD510 0.75 1.32E−02 5 37 Table 32. Providedare the correlations (R) between the expression levels of yieldimproving genes and their homologues in tissues [Flag leaf, Flowermeristem, stem and Flower; Expression sets (Exp)] and the phenotypicperformance in various yield, biomass, growth rate and/or vigorcomponents [Correlation vector (corr.) ID] under stress conditions ornormal conditions across Sorghum accessions. P = p value.

Example 8 Production of Maize Transcriptom and High ThroughputCorrelation Analysis with Yield and NUE Related Parameters Using 60KMaize Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis between plantphenotype and gene expression level, the present inventors utilized amaize oligonucleotide micro-array, produced by Agilent Technologies[Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent(dot) com/Scripts/PDS (dot) asp?lPage=50879]. The array oligonucleotiderepresents about 60,000 maize genes and transcripts.

Correlation of Maize Hybrids Across Ecotypes Grown Under Regular GrowthConditions

Experimental Procedures

12 Maize hybrids were grown in 3 repetitive plots, in field. Maize seedswere planted and plants were grown in the field using commercialfertilization and irrigation protocols. In order to define correlationsbetween the levels of RNA expression with stress and yield components orvigor related parameters, the 12 different maize hybrids were analyzed.Among them, 10 hybrids encompassing the observed variance were selectedfor RNA expression analysis. The correlation between the RNA levels andthe characterized parameters was analyzed using Pearson correlation test[Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot)com/hyperstat/A34739 (dot) html].

Analyzed Maize tissues—All 10 selected maize hybrids were sampled per 3time points (TP2=V6−V8, TPS=R1−R2, TP6=R3−R4). Four types of planttissues [Ear, flag leaf indicated in Table 33 as “leaf”, grain distalpart, and internode] growing under Normal conditions were sampled andRNA was extracted as described above. Each micro-array expressioninformation tissue type has received a Set ID as summarized in Table 33below.

TABLE 33 Maize transcriptom expression sets under normal conditions SetExpression Set ID Ear at reproductive stage (R1-R2) 1 Leaf atreproductive stage (R3-R4) 2 Leaf at vegetative stage (V2-V3) 3Internode at vegetative stage (V2-V3) 4 Internode at reproductive stage(R3-R4) 5 Ear at reproductive stage (R3-R4) 6 Internode at reproductivestage (R1-R2) 7 Leaf at reproductive stage (R1-R2) 8 Provided are theidentification (ID) number of each of the Maize expression sets. Leaf =the leaf below the main ear; Ear = the female flower at the anthesisday; Internodes = internodes located above and below the main ear in theplant.

The following parameters were collected using digital imaging system:

Grain Area (cm²)—At the end of the growing period the grains wereseparated from the ear. A sample of ˜200 grains were weighted,photographed and images were processed using the below described imageprocessing system. The grain area was measured from those images and wasdivided by the number (Num) of grains.

Grain Length and Grain width (cm)—At the end of the growing period thegrains were separated from the ear. A sample of ˜200 grains wereweighted, photographed and images were processed using the belowdescribed image processing system. The sum of grain lengths/or width(longest axis) was measured from those images and was divided by thenumber of grains.

Ear Area (cm²)—At the end of the growing period 5 ears were,photographed and images were processed using the below described imageprocessing system. The Ear area was measured from those images and wasdivided by the number of Ears.

Ear Length and Ear Width (cm)—At the end of the growing period 5 earswere, photographed and images were processed using the below describedimage processing system. The Ear length and width (longest axis) wasmeasured from those images and was divided by the number of ears.

The image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37, Java based image processing software, which wasdeveloped at the U.S. National Institutes of Health and is freelyavailable on the internet at Hypertext Transfer Protocol://rsbweb (dot)nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels(3888×2592 pixels) and stored in a low compression JPEG (JointPhotographic Experts Group standard) format. Next, image processingoutput data for seed area and seed length was saved to text files andanalyzed using the JMP statistical analysis software (SAS institute).

Additional parameters were collected either by sampling 6 plants perplot or by measuring the parameter across all the plants within theplot.

Normalized Grain Weight per plant (gr.)—At the end of the experiment allears from plots within blocks A-C were collected. Six ears wereseparately threshed and grains were weighted, all additional ears werethreshed together and weighted as well. The average grain weight per earwas calculated by dividing the total grain weight by number of totalears per plot (based on plot). In case of 6 ears, the total grainsweight of 6 ears was divided by 6.

Ear FW (gr.)—At the end of the experiment (when ears were harvested)total and 6 selected ears per plots within blocks A-C were collectedseparately. The plants with (total and 6) were weighted (gr.) separatelyand the average ear per plant was calculated for total (Ear FW per plot)and for 6 (Ear FW per plant).

Plant height and Ear height—Plants were characterized for height atharvesting. In each measure, 6 plants were measured for their heightusing a measuring tape. Height was measured from ground level to top ofthe plant below the tassel. Ear height was measured from the groundlevel to the place were the main ear is located.

Leaf number per plant—Plants were characterized for leaf number duringgrowing period at 5 time points. In each measure, plants were measuredfor their leaf number by counting all the leaves of 3 selected plantsper plot.

Relative Growth Rate of leaf number—was calculated using Formula IX(above).

SPAD—Chlorophyll content was determined using a Minolta SPAD 502chlorophyll meter and measurement was performed 64 days post sowing.SPAD meter readings were done on young fully developed leaf. Threemeasurements per leaf were taken per plot. Data were taken after 46 and54 days after sowing (DPS).

Dry weight per plant—At the end of the experiment (when inflorescencewere dry) all vegetative material from plots within blocks A-C werecollected.

Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 70° C. in oven for 48 hours.

Harvest Index (HI) (Maize)—The harvest index was calculated usingFormula X.

Harvest Index=Average grain dry weight per Ear/(Average vegetative dryweight per Ear+Average Ear dry weight).  Formula X

Percent Filled Ear [%]—it was calculated as the percentage of the Eararea with grains out of the total ear.

Filled per Whole Ear—it was calculated as the length of the ear withgrains out of the total ear.

Cob diameter[cm]—The diameter of the cob without grains was measuredusing a ruler.

Kernel Row Number per Ear—The number of rows in each ear was counted.

Experimental Results

12 different maize hybrids were grown and characterized for differentparameters. The correlated parameters are described in Table 34 below.The average for each of the measured parameter was calculated using theJMP software (Tables 35-36) and a subsequent correlation analysis wasperformed (Table 37). Results were then integrated to the database.

TABLE 34 Maize correlated parameters (vectors) Correlated parameter withCorrelation ID Growth Rate Leaf Num (ratio) 1 Plant Height per Plot (cm)2 Ear Height (cm) 3 Leaf Number per Plant(number) 4 Ear Length (cm) 5Percent Filled Ear (percent) 6 Cob Diameter (mm) 7 Kernel Row Number perEar(number) 8 DW per Plant based on 6 (gr). 9 Ear FW per Plant based on6 (gr). 10 Normalized Grain Weight per plant based on 6 (gr). 11 Ears FWper plant based on all (gr). 12 Normalized Grain Weight per Plant basedon all (gr). 13 Ear Area (cm²) 14 Ear Width (cm) 15 Filled per Whole Ear(percent) 16 Grain Area (cm²) 17 Grain Length (cm) 18 Grain Width (cm)19 SPAD 46DPS TP2 20 SPAD 54DPS TP5 21 SPAD 46DPS and SPAD 54DPS:Chlorophyl level after 46 and 54 days after sowing (DPS). “FW” = freshweight; “DW” = dry weight.

TABLE 35 Measured parameters in Maize accessions under normal conditions(lines 1-6) Eco- type/ Cor- re- lation ID No. Line-1 Line-2 Line-3Line-4 Line-5 Line-6 1  0.283 0.221 0.281 0.269 0.306 0.244 2 278.083260.500 275.133 238.500 286.944 224.833 3 135.167 122.333 131.967114.000 135.278 94.278 4  12.000 11.110 11.689 11.778 11.944 12.333 5 19.691 19.055 20.521 21.344 20.920 18.232 6  80.624 86.760 82.14492.708 80.377 82.757 7  28.957 25.078 28.052 25.732 28.715 25.783 8 16.167 14.667 16.200 15.889 16.167 15.167 9 657.500 491.667 641.111580.556 655.556 569.444 10 245.833 208.333 262.222 263.889 272.222177.778 11 140.683 139.536 153.667 176.983 156.614 119.667 12 278.194217.502 288.280 247.879 280.106 175.841 13 153.900 135.882 152.500159.156 140.463 117.135 14  85.058 85.843 90.507 95.953 91.624 72.408 15 5.584 5.151 5.671 5.533 5.728 5.227 16  0.916 0.922 0.927 0.917 0.9080.950 17  0.753 0.708 0.755 0.766 0.806 0.713 18  1.167 1.092 1.1801.205 1.228 1.123 19  0.810 0.814 0.803 0.803 0.824 0.803 20  51.66756.406 53.547 55.211 55.300 59.350 21  54.283 57.178 56.011 59.68254.767 59.144 Table 35. Provided are the values of each of theparameters (as described above) measured in maize accessions (Seed ID)under regular growth conditions. Growth conditions are specified in theexperimental procedure section.

TABLE 36 Additional measured parameters in Maize accessions underregular growth conditions (lines 7-12) Eco- type/ Corre- lation Line-Line- ID No. Line-7 Line-8 Line-9 Line-10 11 12 1 0.244 0.266 0.1940.301 2 264.444 251.611 163.778 278.444 3 120.944 107.722 60.444 112.5004 12.444 12.222 9.278 12.556 5 19.017 18.572 16.689 21.702 6 73.24881.061 81.056 91.601 7 26.432 25.192 26.668 8 16.000 14.833 14.26715.389 9 511.111 544.444 574.167 522.222 10 188.889 197.222 141.111261.111 11 119.692 133.508 54.316 173.231 12 192.474 204.700 142.716264.236 13 123.237 131.266 40.844 170.662 14 74.032 76.534 55.201 95.36015 5.221 5.328 4.120 5.577 16 0.873 0.939 0.796 0.958 17 0.714 0.7530.502 0.762 18 1.139 1.134 0.921 1.180 19 0.791 0.837 0.675 0.812 2058.483 55.876 53.856 59.747 52.983 49.994 21 57.994 60.356 51.394 61.13954.767 53.344 Table 36. Provided are the values of each of theparameters (as described above) measured in maize accessions (Seed ID)under regular growth conditions. Growth conditions are specified in theexperimental procedure section.

TABLE 37 Correlation between the expression level of selected LYD genesof some embodiments of the invention in various tissues and thephenotypic performance under normal across maize accessions Exp. Corr.Set Exp. Corr. Set Gene Name R P value set ID Gene Name R P value set IDLYD391 0.75 3.14E−02 5 19 LYD391 0.82 2.28E−02 7 14 LYD391 0.75 5.23E−027 13 LYD391 0.81 2.86E−02 7 2 LYD391 0.92 3.41E−03 7 3 LYD391 0.822.50E−02 7 12 LYD391 0.77 4.39E−02 7 10 LYD391 0.74 5.55E−02 7 11 LYD3910.93 6.47E−03 1 7 LYD391 0.80 5.59E−02 6 19 LYD503 0.81 2.75E−02 7 4LYD503 0.81 2.88E−02 7 16 LYD503 0.76 4.79E−02 7 2 LYD503 0.86 1.26E−027 19 LYD503 0.89 6.73E−03 8 4 LYD503 0.88 9.13E−03 8 21 LYD503 0.717.16E−02 8 18 LYD503 0.85 1.61E−02 8 16 LYD503 0.72 6.56E−02 8 17 LYD5030.71 7.11E−02 8 19 LYD503 0.75 5.03E−02 1 14 LYD503 0.71 7.51E−02 1 13LYD503 0.79 3.45E−02 1 2 LYD503 0.88 9.31E−03 1 3 LYD503 0.70 7.77E−02 115 LYD503 0.82 2.43E−02 1 12 LYD503 0.73 6.20E−02 1 10 LYD503 0.911.30E−02 6 4 Table 37. “Corr. ID “-correlation set ID according to thecorrelated parameters Table 34 above. “Exp. Set”-Expression set. “R” =Pearson correlation coefficient; “P” = p value.

Example 9 Production of Soybean (Glycine max) Transcriptom and HighThroughput Correlation Analysis with Yield Parameters Using 44K B.Soybean Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis, the presentinventors utilized a Soybean oligonucleotide micro-array, produced byAgilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot)chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?IPage=50879]. Thearray oligonucleotide represents about 42,000 Soybean genes andtranscripts. In order to define correlations between the levels of RNAexpression with yield components or plant architecture relatedparameters or plant vigor related parameters, various plantcharacteristics of 29 different Glycine max varieties were analyzed and12 varieties were further used for RNA expression analysis. Thecorrelation between the RNA levels and the characterized parameters wasanalyzed using Pearson correlation test.

Correlation of Glycine max Genes' Expression Levels with PhenotypicCharacteristics Across Ecotype

Experimental Procedures

29 Soybean varieties were grown in three repetitive plots, in field.Briefly, the growing protocol was as follows: Soybean seeds were sown insoil and grown under normal conditions until harvest. In order to definecorrelations between the levels of RNA expression with yield componentsor plant architecture related parameters or vigor related parameters, 12different Soybean varieties (out of 29 varieties) were analyzed and usedfor gene expression analyses. Analysis was performed at twopre-determined time periods: at pod set (when the soybean pods areformed) and at harvest time (when the soybean pods are ready forharvest, with mature seeds). Table 39 describes the soybean correlatedparameters. The average for each of the measured parameter wascalculated using the JMP software (Tables 40-41) and a subsequentcorrelation analysis was performed (Table 42). Results were thenintegrated to the database.

TABLE 38 Soybean transcriptom expression sets Expression Set Set IDApical meristem at vegetative stage under normal growth condition 1 Leafat vegetative stage under normal growth condition 2 Leaf at floweringstage under normal growth condition 3 Leaf at pod setting stage undernormal growth condition 4 Root at vegetative stage under normal growthcondition 5 Root at flowering stage under normal growth condition 6 Rootat pod setting stage under normal growth condition 7 Stem at vegetativestage under normal growth condition 8 Stem at pod setting stage undernormal growth condition 9 Flower bud at flowering stage under normalgrowth condition 10 Pod (R3-R4) at pod setting stage under normal growthcondition 11 Provided are the soybean transcriptom expression sets.

RNA extraction—All 12 selected Soybean varieties were sample pertreatment. Plant tissues [leaf, root. Stem. Pod, apical meristem. Flowerbuds] growing under normal conditions were sampled and RNA was extractedas described above.

The collected data parameters were as follows:

Main branch base diameter [mm] at pod set—the diameter of the base ofthe main branch (based diameter) average of three plants per plot.

Fresh weight[gr/plant] at pod set—total weight of the vegetative portionabove ground (excluding roots) before drying at pod set, average ofthree plants per plot.

Dry weight [gr/plant] at pod set—total weight of the vegetative portionabove ground (excluding roots) after drying at 70° C. in oven for 48hours at pod set, average of three plants per plot.

Total number of nodes with pods on lateral branches[value/plant]—counting of nodes which contain pods in lateral branchesat pod set, average of three plants per plot.

Number of lateral branches at pod set [value/plant]—counting number oflateral branches at pod set, average of three plants per plot.

Total weight of lateral branches at pod set [gr/plant]—weight alllateral branches at pod set, average of three plants per plot.

Total weight of pods on main stem at pod set [gr/plant]—weight all podson main stem at pod set, average of three plants per plot.

Total number of nodes on main stem [value/plant]—count of number ofnodes on main stem starting from first node above ground, average ofthree plants per plot.

Total number of pods with 1 seed on lateral branches at pod set[value/plant]—count the number of pods containing 1 seed in all lateralbranches at pod set, average of three plants per plot.

Total number of pods with 2 seeds on lateral branches at pod set[value/plant]—count the number of pods containing 2 seeds in all lateralbranches at pod set, average of three plants per plot.

Total number of pods with 3 seeds on lateral branches at pod set[value/plant]—count the number of pods containing 3 seeds in all lateralbranches at pod set, average of three plants per plot.

Total number of pods with 4 seeds on lateral branches at pod set[value/plant]—count the number of pods containing 4 seeds in all lateralbranches at pod set, average of three plants per plot.

Total number of pods with 1 seed on main stem at pod set[value/plant]—count the number of pods containing 1 seed in main stem atpod set, average of three plants per plot.

Total number of pods with 2 seeds on main stem at pod set[value/plant]—count the number of pods containing 2 seeds in main stemat pod set, average of three plants per plot.

Total number of pods with 3 seeds on main stem at pod set[value/plant]—count the number of pods containing 3 seeds in main stemat pod set, average of three plants per plot.

Total number of pods with 4 seeds on main stem at pod set[value/plant]—count the number of pods containing 4 seeds in main stemat pod set, average of three plants per plot.

Total number of seeds per plant at pod set [value/plant]—count number ofseeds in lateral branches and main stem at pod set, average of threeplants per plot.

Total number of seeds on lateral branches at pod set [value/plant]—counttotal number of seeds on lateral branches at pod set, average of threeplants per plot.

Total number of seeds on main stem at pod set [value/plant]—count totalnumber of seeds on main stem at pod set, average of three plants perplot.

Plant height at pod set[cm/plant]—total length from above ground tillthe tip of the main stem at pod set, average of three plants per plot.

Plant height at harvest[cm/plant]—total length from above ground tillthe tip of the main stem at harvest, average of three plants per plot.

Total weight of pods on lateral branches at pod set [gr/plant]—weight ofall pods on lateral branches at pod set, average of three plants perplot.

Ratio of the number of pods per node on main stem at pod set—calculatedin formula XI, average of three plants per plot.

Total number of pods on main stem/Total number of nodes on main stem,average of three plants per plot.  Formula XI

Ratio of total number of seeds in main stem to number of seeds onlateral branches—calculated in formula XII, average of three plants perplot.

Total number of seeds on main stem at pod set/Total number of seeds onlateral branches at pod set.  Formula XII

Total weight of pods per plant at pod set [gr/plant]—weight all pods onlateral branches and main stem at pod set, average of three plants perplot.

Days till 50% flowering [days]—number of days till 50% flowering foreach plot.

Days till 100% flowering [days]—number of days till 100% flowering foreach plot.

Maturity [days]—measure as 95% of the pods in a plot have ripened(turned 100% brown). Delayed leaf drop and green stems are notconsidered in assigning maturity. Tests are observed 3 days per week,every other day, for maturity. The maturity date is the date that 95% ofthe pods have reached final color. Maturity is expressed in days afterAugust 31 [according to the accepted definition of maturity in USA,Descriptor list for SOYBEAN, Hypertext Transfer Protocol://World WideWeb (dot) ars-grin (dot) gov/cgi-bin/npgs/html/desclist (dot) pl?51].

Seed quality [ranked 1-5]—measure at harvest, A visual estimate based onseveral hundred seeds. Parameter is rated according to the followingscores considering the amount and degree of wrinkling, defective coat(cracks), greenishness, and moldy or other pigment. Rating is 1-verygood, 2-good, 3-fair, 4-poor, 5-very poor.

Lodging [ranked 1-5]—is rated at maturity per plot according to thefollowing scores: 1-most plants in a plot are erected, 2-All plantsleaning slightly or a few plants down, 3-all plants leaning moderately,or 25%-50% down, 4-all plants leaning considerably, or 50%-80% down,5-most plants down. Note: intermediate score such as 1.5 are acceptable.

Seed size [gr.]—weight of 1000 seeds per plot normalized to 13%moisture, measure at harvest.

Total weight of seeds per plant [gr./plant]—calculated at harvest (per 2inner rows of a trimmed plot) as weight in grams of cleaned seedsadjusted to 13% moisture and divided by the total number of plants intwo inner rows of a trimmed plot.

Yield at harvest [bushels/hectare]—calculated at harvest (per 2 innerrows of a trimmed plot) as weight in grams of cleaned seeds, adjusted to13% moisture, and then expressed as bushels per acre.

Average lateral branch seeds per pod [number]—Calculate Num of Seeds onlateral branches—at pod set and divide by the Number of Total number ofpods with seeds on lateral branches—at pod set.

Average main stem seeds per pod[number]—Calculate Total Number of Seedson main stem at pod set and divide by the Number of Total number of podswith seeds on main stem at pod setting.

Main stem average internode length [cm]—Calculate Plant height at podset and divide by the Total number of nodes on main stem at pod setting.

Total number of pods with seeds on main stem [number]—count all podscontaining seeds on the main stem at pod setting.

Total number of pods with seeds on lateral branches [number]—count allpods containing seeds on the lateral branches at pod setting.

Total number of pods per plant at pod set [number]—count pods on mainstem and lateral branches at pod setting.

Experimental Results

Twelve different Soybean varieties were grown and characterized for 40parameters as specified in Table 39 below. The average for each of themeasured parameters was calculated using the JMP software and values aresummarized in Tables 40-41 below. Subsequent correlation analysisbetween the various transcriptom expression sets and the averageparameters was conducted (Table 42). Results were then integrated to thedatabase.

TABLE 39 Soybean correlated parameters (vectors) Correlated parameterwith Correlation ID Base diameter at pod set (mm) 1 DW at pod set (gr.)2 fresh weight at pod set (gr.) 3 Total number of nodes with pods onlateral branches (number) 4 Num of lateral branches (number) 5 Totalweight of lateral branches at pod set (gr.) 6 Total weight of pods onmain stem at pod set (gr.) 7 Total number of nodes on main stem (number)8 Total no of pods with 1 seed on lateral branch (number) 9 Num of podswith 1 seed on main stem at pod set (number) 10 Total no of pods with 2seed on lateral branch (number) 11 Num of pods with 2 seed on main stem(number) 12 Total no of pods with 3 seed on lateral branch (number) 13Num of pods with 3 seed on main stem (number) 14 Total no of pods with 4seed on lateral branch (number) 15 Num of pods with 4 seed on main stem(number) 16 Total number of seeds per plant 17 Total Number of Seeds onlateral branches 18 Total Number of Seeds on main stem at pod set 19Plant height at pod set (cm) 20 Total weight of pods on lateral branches(gr.) 21 Ratio number of pods per node on main stem (ratio) 22 Rationumber of seeds per main stem to seeds per lateral branch (ratio) 23Total weight of pods per plant (gr.) 24 50 percent flowering (days) 25Maturity (days) 26 100 percent flowering (days) 27 Plant height atharvest (cm) 28 Seed quality (score 1-5) 29 Total weight of seeds perplant (gr./plant) 30 Seed size (gr.) 31 Lodging (score 1-5) 32 yield atharvest (bushel/hectare) 33 Average lateral branch seeds per pod(number) 34 Average main stem seeds per pod (number) 35 Total number ofpods with seeds on main stem at pod set (number) 36 Num pods with seedson lateral branches-at pod set (number) 37 Total number of pods perplant at pod set (number) 38 Main stem average internode length(cm/number) 39 Corrected Seed size (gr.) 40

TABLE 40 Measured parameters in Soybean varieties (lines1-6) Ecotype/Correlation ID No. Line 1 Line 2 Line 3 Line 4 Line 5 Line 6 1 8.33 9.549.68 8.11 8.82 10.12 2 53.67 50.33 38.00 46.17 60.83 55.67 3 170.89198.22 152.56 163.89 224.67 265.00 4 23.00 16.00 23.11 33.00 15.22 45.255 9.00 8.67 9.11 9.89 7.67 17.56 6 67.78 63.78 64.89 74.89 54.00 167.227 22.11 14.33 16.00 15.00 33.78 9.00 8 16.56 16.78 16.11 18.11 16.7817.11 9 1.56 3.00 1.78 1.78 5.67 5.63 10 1.11 4.38 1.44 1.44 4.56 1.6711 17.00 18.75 26.44 32.33 21.56 33.50 12 16.89 16.25 13.22 16.89 27.008.11 13 38.44 2.00 26.44 31.33 8.89 82.00 14 29.56 1.75 19.78 22.3311.67 22.78 15 0.00 0.00 0.00 0.00 0.00 1.50 16 0.00 0.00 0.11 0.11 0.000.44 17 274.44 99.78 221.67 263.11 169.00 412.50 18 150.89 55.89 134.00160.44 75.44 324.63 19 123.56 43.89 87.67 102.67 93.56 88.00 20 86.7869.56 62.44 70.89 69.44 63.89 21 26.00 14.89 20.11 20.11 21.11 30.25 222.87 1.38 2.13 2.26 2.60 1.87 23 0.89 0.90 0.87 0.89 2.32 0.37 24 48.1129.22 36.11 35.11 54.89 38.88 25 61.00 65.33 60.67 61.00 54.67 68.33 2624.00 43.67 30.33 30.33 38.33 40.00 27 67.33 71.67 67.67 67.33 60.0074.00 28 96.67 76.67 67.50 75.83 74.17 76.67 29 2.33 3.50 3.00 2.17 2.832.00 30 15.09 10.50 17.23 16.51 12.06 10.25 31 89.00 219.33 93.00 86.00191.33 71.33 32 1.67 1.83 1.17 1.67 2.67 2.83 33 47.57 43.77 50.37 56.3044.00 40.33 34 2.67 1.95 2.43 2.53 2.13 2.68 35 2.60 1.89 2.52 2.53 2.172.59 36 47.56 23.11 34.56 40.78 43.22 33.00 37 57.00 28.56 54.67 65.4436.11 122.63 38 104.56 51.67 89.22 106.22 79.33 155.63 39 5.24 4.15 3.913.92 4.15 3.74 40 89.00 * 93.00 86.00 * 71.33

TABLE 41 Measured parameters in Soybean varieties (lines 7-12) Ecotype/Correlation ID No. Line 7 Line 8 Line 9 Line 10 Line 11 Line 12 1 8.468.09 8.26 7.73 8.16 7.89 2 48.00 52.00 44.17 52.67 56.00 47.50 3 160.67196.33 155.33 178.11 204.44 164.22 4 8.25 25.44 21.88 16.33 22.56 24.225 11.67 12.11 8.00 9.11 6.78 10.00 6 45.44 83.22 64.33 52.00 76.89 67.007 9.03 16.00 15.89 14.56 30.44 18.00 8 18.78 18.89 16.78 21.11 19.3320.78 9 2.88 3.00 1.25 2.67 1.78 3.00 10 4.00 4.33 2.11 1.89 3.44 1.2211 8.50 22.78 21.75 10.67 23.78 25.67 12 21.33 17.67 20.33 16.11 28.1116.56 13 9.00 42.11 32.75 25.67 45.00 44.33 14 11.11 28.22 24.11 36.4439.67 32.33 15 0.00 0.33 0.00 1.11 0.00 0.00 16 0.00 0.56 0.00 3.89 0.000.00 17 136.00 302.78 260.50 264.44 363.00 318.67 18 46.88 176.22 143.00105.44 184.33 187.33 19 80.00 126.56 115.11 159.00 178.67 131.33 2089.78 82.11 70.56 101.67 79.56 67.22 21 4.13 20.11 17.00 9.22 28.1122.56 22 1.98 2.71 2.78 2.75 3.70 2.84 23 3.90 0.78 1.18 1.98 1.03 0.8324 14.25 36.11 32.75 23.78 58.56 40.56 25 66.50 65.67 62.33 67.67 61.6764.33 26 41.00 38.33 31.00 39.00 27.33 32.67 27 73.00 72.33 68.67 73.6768.00 70.67 28 101.67 98.33 75.83 116.67 76.67 71.67 29 3.50 2.50 2.172.33 2.17 2.17 30 7.30 11.38 15.68 10.83 12.98 15.16 31 88.00 75.0080.67 75.67 76.33 77.33 32 2.67 2.50 1.83 3.50 3.33 1.50 33 34.23 44.2753.67 42.47 43.60 52.20 34 2.12 2.58 2.58 2.67 2.62 2.58 35 2.22 2.492.47 2.71 2.51 2.61 36 36.44 50.78 43.63 58.33 71.22 50.11 37 20.3868.22 55.75 40.11 70.56 73.00 38 61.00 119.00 103.25 98.44 141.78 123.1139 4.80 4.36 4.20 4.82 4.12 3.83 40 88.00 75.00 80.67 75.67 76.33 77.33

TABLE 42 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across soybean varieties Corr. Corr.Gene Name R P value Exp. set Set ID Gene Name R P value Exp. set Set IDLYD437 0.71 2.10E−02 5 23 LYD437 0.76 2.79E−02 9 14 LYD437 0.84 9.58E−039 19 LYD437 0.85 7.25E−03 9 22 LYD437 0.73 7.53E−03 4 30 LYD437 0.719.26E−03 4 33 LYD438 0.86 1.38E−03 8 30 LYD438 0.81 4.31E−03 8 33 LYD4380.71 1.02E−02 10 4 LYD438 0.71 9.94E−03 10 17 LYD439 0.79 6.84E−03 7 11LYD439 0.74 1.43E−02 8 3 LYD439 0.79 7.01E−03 8 15 LYD439 0.72 2.01E−028 9 LYD439 0.82 4.05E−03 8 31 LYD439 0.78 2.19E−02 9 30 LYD439 0.733.97E−02 9 33 LYD439 0.75 3.09E−02 9 19 LYD439 0.82 1.18E−02 9 22 LYD4390.72 4.40E−02 9 7 LYD439 0.76 6.38E−03 2 31 LYD439 0.71 1.02E−02 10 3LYD440 0.84 2.29E−03 7 23 LYD440 0.78 8.30E−03 7 30 LYD440 0.76 1.02E−027 33 LYD440 0.73 1.67E−02 7 31 LYD440 0.76 4.52E−03 11 30 LYD440 0.792.22E−03 11 33 LYD440 0.81 4.12E−03 5 7 LYD440 0.76 1.04E−02 8 15 LYD4400.71 4.81E−02 9 23 LYD440 0.75 3.33E−02 9 33 LYD440 0.76 2.84E−02 9 7LYD440 0.74 8.79E−03 2 31 LYD440 0.79 2.00E−03 4 7 LYD441 0.71 2.10E−027 18 LYD441 0.80 5.65E−03 7 3 LYD441 0.87 9.46E−04 7 6 LYD441 0.779.62E−03 7 4 LYD441 0.76 4.21E−03 11 30 LYD441 0.83 7.65E−04 11 33LYD441 0.75 1.26E−02 5 3 LYD441 0.83 2.98E−03 5 6 LYD441 0.91 2.85E−04 51 LYD441 0.72 1.88E−02 8 23 LYD441 0.81 1.42E−02 9 25 LYD441 0.848.80E−03 9 15 LYD441 0.71 5.03E−02 9 6 LYD441 0.93 8.95E−04 9 5 LYD4410.77 2.44E−02 9 27 LYD441 0.83 1.08E−02 9 9 LYD441 0.81 2.55E−03 2 31LYD441 0.77 3.63E−03 10 15 LYD442 0.77 3.12E−03 11 30 LYD442 0.863.26E−04 11 33 LYD442 0.82 1.23E−02 9 5 LYD442 0.80 1.92E−03 4 25 LYD4420.78 2.57E−03 4 27 LYD443 0.74 1.49E−02 7 26 LYD443 0.77 8.47E−03 7 3LYD443 0.78 7.44E−03 7 1 LYD443 0.81 4.94E−03 7 9 LYD443 0.78 3.05E−0311 30 LYD443 0.76 4.41E−03 11 33 LYD443 0.77 8.92E−03 8 15 LYD443 0.712.04E−02 8 28 LYD443 0.73 1.60E−02 8 6 LYD443 0.83 3.21E−03 8 5 LYD4430.80 1.64E−02 9 12 LYD443 0.77 2.49E−02 9 31 LYD443 0.80 2.99E−03 2 31LYD443 0.74 5.78E−03 10 32 LYD445 0.74 1.39E−02 5 14 LYD445 0.895.63E−04 5 13 LYD445 0.88 8.05E−04 5 18 LYD445 0.80 5.31E−03 5 11 LYD4450.80 5.46E−03 5 4 LYD445 0.94 7.06E−05 5 17 LYD445 0.71 2.28E−02 5 9LYD445 0.77 9.00E−03 8 13 LYD445 0.77 8.50E−03 8 18 LYD445 0.72 1.84E−028 4 LYD445 0.73 1.62E−02 8 17 LYD445 0.87 5.49E−03 9 30 LYD445 0.753.37E−02 9 33 LYD445 0.73 3.82E−02 9 12 LYD445 0.80 1.61E−02 9 22 LYD4450.74 3.72E−02 9 7 LYD445 0.75 4.89E−03 4 9 LYD445 0.74 6.41E−03 1 3LYD445 0.80 1.66E−03 1 15 LYD445 0.76 3.95E−03 1 6 LYD445 0.71 9.11E−031 4 LYD445 0.80 1.87E−03 10 13 LYD445 0.76 3.87E−03 10 18 LYD445 0.838.99E−04 10 17 LYD446 0.92 1.56E−04 5 14 LYD446 0.90 4.07E−04 5 19LYD446 0.75 1.29E−02 5 22 LYD446 0.77 9.54E−03 5 17 LYD446 0.71 2.07E−028 14 LYD446 0.71 2.21E−02 8 30 LYD446 0.84 2.62E−03 8 13 LYD446 0.851.64E−03 8 18 LYD446 0.76 1.05E−02 8 3 LYD446 0.84 2.44E−03 8 15 LYD4460.92 1.63E−04 8 6 LYD446 0.73 1.65E−02 8 5 LYD446 0.89 5.06E−04 8 4LYD446 0.74 1.35E−02 8 17 LYD446 0.72 4.46E−02 9 30 LYD446 0.76 2.75E−029 33 LYD446 0.73 7.17E−03 10 13 LYD446 0.76 3.96E−03 10 18 LYD446 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LYD446 0.81 4.93E−03 5 35 LYD446 0.84 2.19E−03 5 36LYD446 0.79 6.69E−03 5 34 LYD446 0.74 1.45E−02 5 38 LYD446 0.86 1.56E−038 37 LYD446 0.73 1.72E−02 8 35 LYD446 0.74 1.47E−02 8 34 LYD446 0.741.36E−02 8 38 LYD446 0.77 3.47E−03 10 37 LYD447 0.70 2.36E−02 5 37LYD447 0.81 4.59E−03 5 38 LYD447 0.75 1.25E−02 8 37 LYD447 0.71 2.04E−028 35 LYD448 0.72 8.31E−03 10 37 LYD449 0.83 2.77E−03 5 37 LYD449 0.779.16E−03 5 38 LYD449 0.84 2.35E−03 8 37 LYD449 0.74 1.39E−02 8 38 LYD4490.82 9.71E−04 10 37 LYD449 0.73 6.85E−03 10 38 LYD450 0.72 8.82E−03 1038 LYD452 0.73 1.56E−02 5 37 LYD452 0.84 2.35E−03 8 37 LYD452 0.741.39E−02 8 38 LYD452 0.81 1.55E−03 10 37 LYD452 0.72 7.82E−03 10 38LYD455 0.83 1.08E−02 9 36 LYD458 0.79 6.01E−03 8 35 LYD458 0.71 2.25E−028 34 LYD458 0.73 9.99E−03 2 35 LYD459 0.74 1.53E−02 7 37 LYD459 0.721.78E−02 7 35 LYD459 0.79 6.83E−03 7 34 LYD459 0.71 2.24E−02 7 38 LYD4590.80 5.82E−03 5 37 LYD459 0.76 3.02E−02 9 37 LYD459 0.87 4.49E−04 2 35LYD459 0.82 1.84E−03 2 34 LYD459 0.83 8.59E−04 10 37 LYD460 0.741.42E−02 5 37 LYD461 0.82 3.93E−03 5 36 LYD462 0.85 1.90E−03 8 37 LYD4650.72 8.92E−03 10 37 LYD465 0.76 4.04E−03 10 34 LYD466 0.78 2.17E−02 9 37LYD466 0.91 1.89E−03 9 35 LYD466 0.85 8.07E−03 9 34 LYD466 0.78 2.33E−029 38 LYD468 0.70 1.06E−02 1 34 LYD469 0.88 1.65E−04 1 36 LYD469 0.811.53E−03 10 37 LYD471 0.72 1.99E−02 8 35 LYD471 0.73 7.63E−03 10 37LYD471 0.71 9.52E−03 10 35 LYD471 0.72 8.58E−03 10 34 LYD471 0.811.48E−03 10 38 LYD473 0.70 2.40E−02 8 35 LYD473 0.72 1.86E−02 8 34LYD511 0.72 4.53E−02 9 37 LYD513 0.92 1.56E−04 7 35 LYD513 0.90 3.48E−047 34 LYD513 0.72 1.82E−02 7 38 LYD514 0.75 1.24E−02 8 35 LYD514 0.745.59E−03 4 36 LYD515 0.79 2.45E−03 10 36 LYD516 0.72 4.34E−02 9 37LYD516 0.75 4.91E−03 10 37 LYD516 0.71 9.74E−03 10 38 LYD517 0.721.83E−02 7 36 LYD517 0.81 4.61E−03 8 37 LYD517 0.78 7.26E−03 8 38 LYD5170.86 6.47E−03 9 37 LYD517 0.79 1.93E−02 9 38 LYD518 0.81 1.40E−03 11 36LYD518 0.80 5.27E−03 5 37 LYD519 0.81 4.93E−03 5 35 LYD519 0.84 2.19E−035 36 LYD519 0.80 5.26E−03 5 34 LYD519 0.87 9.29E−04 5 38 LYD519 0.938.53E−05 8 37 LYD519 0.79 6.99E−03 8 38 LYD519 0.74 6.38E−03 10 37LYD437 0.74 3.55E−02 7 40 LYD438 0.74 3.46E−02 7 40 LYD438 0.79 6.15E−034 40 LYD438 0.71 2.21E−02 1 40 LYD440 0.74 5.82E−02 9 40 LYD440 0.721.90E−02 10 40 LYD447 0.71 2.25E−02 11 40 LYD447 0.72 1.97E−02 1 40LYD448 0.78 2.31E−02 5 40 LYD449 0.83 1.02E−02 7 40 LYD449 0.76 1.77E−022 40 LYD449 0.77 9.76E−03 4 40 LYD455 0.73 1.62E−02 11 40 LYD465 0.736.40E−02 9 40 LYD514 0.73 1.71E−02 1 40 LYD517 0.74 1.47E−02 11 40 Table42. Provided are the correlations (R) between the expression levelsyield improving genes and their homologs in various tissues [Expression(Exp) sets] and the phenotypic performance [yield, biomass, and plantarchitecture (Correlation vector (Corr.) ID)] under normal conditionsacross soybean varieties. P = p value.

Example 10 Production of Barley Transcriptom and High ThroughputCorrelation Analysis Using 44K Barley Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis, the presentinventors utilized a Barley oligonucleotide micro-array, produced byAgilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot)chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?lPage=50879]. Thearray oligonucleotide represents about 47,500 Barley genes andtranscripts. In order to define correlations between the levels of RNAexpression and yield or vigor related parameters, various plantcharacteristics of 25 different Barley accessions were analyzed. Amongthem, 13 accessions encompassing the observed variance were selected forRNA expression analysis. The correlation between the RNA levels and thecharacterized parameters was analyzed using Pearson correlation test[Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot)com/hyperstat/A34739 (dot) html].

Experimental Procedures

Five tissues at different developmental stages [meristem, flower,booting spike, stem, flag leaf], representing different plantcharacteristics, were sampled and RNA was extracted as describedhereinabove under “GENERAL EXPERIMENTAL AND BIOINFORMATICS METHODS”.

For convenience, each micro-array expression information tissue type hasreceived a Set ID as summarized in Table 43 below.

TABLE 43 Barley transcriptom expression sets Expression Set Set IDbooting spike at flowering stage 1 Stem at flowering stage 2 floweringspike at flowering stage 3 Meristem at flowering stage 4 Provided arethe identification (ID) digits of each of the Barley expression sets.

Barley yield components and vigor related parameters assessment—13Barley accessions in 4 repetitive blocks (named A, B, C, and D), eachcontaining 4 plants per plot were grown at net house. Plants werephenotyped on a daily basis following the standard descriptor of barley(Table 44, below). Harvest was conducted while 50% of the spikes weredry to avoid spontaneous release of the seeds. Plants were separated tothe vegetative part and spikes, of them, 5 spikes were threshed (grainswere separated from the glumes) for additional grain analysis such assize measurement, grain count per spike and grain yield per spike. Allmaterial was oven dried and the seeds were threshed manually from thespikes prior to measurement of the seed characteristics (weight andsize) using scanning and image analysis. The image analysis systemincluded a personal desktop computer (Intel P4 3.0 GHz processor) and apublic domain program—ImageJ 1.37 (Java based image processing program,which was developed at the U.S. National Institutes of Health and freelyavailable on the internet [Hypertext Transfer Protocol://rsbweb (dot)nih (dot) gov/]. Next, analyzed data was saved to text files andprocessed using the JMP statistical analysis software (SAS institute).

TABLE 44 Barley standard descriptors Trait Parameter Range DescriptionGrowth habit Scoring 1-9 Prostrate (1) or Erect (9) Hairiness of ScoringP (Presence)/A Absence (1) or Presence (2) basal leaves (Absence) StemScoring 1-5 Green (1), Basal only or Half or more pigmentation (5) Daysto Days Days from sowing to emergence of Flowering awns Plant heightCentimeter (cm) Height from ground level to top of the longest spikeexcluding awns Spikes per plant Number Terminal Counting Spike lengthCentimeter (cm) Terminal Counting 5 spikes per plant Grains per spikeNumber Terminal Counting 5 spikes per plant Vegetative dry GramOven-dried for 48 hours at 70° C. weight Spikes dry Gram Oven-dried for48 hours at 30° C. weight

At the end of the experiment (50% of the spikes were dry) all spikesfrom plots within blocks A-D were collected, and the followingmeasurements were performed:

(i) Grains per spike—The total number of grains from 5 spikes that weremanually threshed was counted. The average grain per spike wascalculated by dividing the total grain number by the number of spikes.

(ii) Grain average size (cm)—The total grains from 5 spikes that weremanually threshed were scanned and images were analyzed using thedigital imaging system. Grain scanning was done using Brother scanner(model DCP-135), at the 200 dpi resolution and analyzed with Image Jsoftware. The average grain size was calculated by dividing the totalgrain size by the total grain number.

(iii) Grain average weight (mgr)—The total grains from 5 spikes thatwere manually threshed were counted and weight. The average weight wascalculated by dividing the total weight by the total grain number.

(iv) Grain yield per spike (gr)—The total grains from 5 spikes that weremanually threshed were weight. The grain yield was calculated bydividing the total weight by the spike number.

(v) Spike length analysis—The five chosen spikes per plant were measuredusing measuring tape excluding the awns.

(vi) Spike number analysis—The spikes per plant were counted.

Additional parameters were measured as follows:

Growth habit scoring—At growth stage 10 (booting), each of the plantswas scored for its growth habit nature. The scale that was used was 1for prostate nature till 9 for erect.

Hairiness of basal leaves—At growth stage 5 (leaf sheath strongly erect;end of tillering), each of the plants was scored for its hairinessnature of the leaf before the last. The scale that was used was 1 forprostate nature till 9 for erect.

Plant height—At harvest stage (50% of spikes were dry), each of theplants was measured for its height using measuring tape. Height wasmeasured from ground level to top of the longest spike excluding awns.

Days to flowering—Each of the plants was monitored for flowering date.Days of flowering was calculated from sowing date till flowering date.

Stem pigmentation—At growth stage 10 (booting), each of the plants wasscored for its stem color. The scale that was used was 1 for green till5 for full purple.

Vegetative dry weight and spike yield—At the end of the experiment (50%of the spikes were dry) all spikes and vegetative material from plotswithin blocks A-D are collected. The biomass and spikes weight of eachplot was separated, measured and divided by the number of plants.

Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 70° C. in oven for 48 hours;

Spike yield per plant=total spike weight per plant (gr.) after drying at30° C. in oven for 48 hours.

TABLE 45 Barley correlated parameters (vectors) Correlated parameterwith Correlation ID Spikes per plant (number) 1 days to flowering (days)2 Grain weight (gr) 3 Spike length (cm) 4 Grains Size (mm) 5 Grains perspike (number) 6 Growth habit (score 1-9) 7 Hairiness of basalleaves(score 1-9) 8 Plant height (cm) 9 Seed Yield of 5 Spikes (gr.) 10Stem pigmentation(score 1-5) 11 Vegetative dry weight (gr.) 12 Providedare the Barley correlated parameters (vectors).

Experimental Results

13 different Barley accessions were grown and characterized for 12parameters as described above. The average for each of the measuredparameter was calculated using the JMP software and values aresummarized in Tables 46 and 47 below. Subsequent correlation analysisbetween the various transcriptom expression sets (Table 43) and theaverage parameters (Tables 46-47) was conducted. Follow, results wereintegrated to the database (Table 48 below).

TABLE 46 Measured parameters of correlation Ids in Barley accessions(lines 1-6) Ecotype/ Correla- tion ID No. Line-1 Line-2 Line-3 Line-4Line-5 Line-6  1  48.846  48.273  37.417  61.917  33.273  41.692  2 62.400  64.083  65.154  58.917  63.000  70.538  3  35.046  28.065 28.761  17.869  41.216  29.734  4  12.036  10.932  11.825  9.900 11.682  11.532  5  0.265  0.229  0.244  0.166  0.295  0.275  6  20.229 17.983  17.267  17.733  14.467  16.783  7  2.600  2.000  1.923  3.167 4.333  2.692  8  1.533  1.333  1.692  1.083  1.417  1.692  9 134.267130.500 138.769 114.583 127.750 129.385 10  3.559  2.538  2.583  1.574 3.030  2.517 11  1.133  2.500  1.692  1.750  2.333  2.308 12  78.871 66.141  68.491  53.389  68.300  74.173 Provided are the values of eachof the parameters measured in Barley accessions according to thecorrelation identifications (see Table 45).

TABLE 47 Barley accessions, additional measured parameters (lines 7-13)Ecotype/ Correlation ID No. Line-7 Line-8 Line-9 Line-10 Line-11 Line-12Line-13 1 40.000 40.625 62.000 49.333 50.600 43.091 51.400 2 52.80060.875 58.100 53.000 60.400 64.583 56.000 3 25.224 34.994 20.580 27.50137.126 29.564 19.583 4 8.863 11.216 11.108 8.583 10.179 10.505 9.803 50.220 0.278 0.187 0.224 0.273 0.271 0.179 6 12.120 14.067 21.540 12.10013.400 15.283 17.067 7 3.600 3.500 3.000 3.667 2.467 3.500 3.000 8 1.3001.188 1.000 1.167 1.600 1.083 1.167 9 103.889 121.625 126.800 99.833121.400 118.417 117.167 10 1.549 2.624 2.300 1.678 2.677 2.353 1.673 111.700 2.188 2.300 1.833 3.067 1.583 2.167 12 35.354 58.334 62.230 38.32268.306 56.148 42.682 Provided are the values of each of the parametersmeasured in Barley accessions according to the correlationidentifications (see Table 45).

TABLE 48 Correlation between the expression level of the selectedpolynucleotides of the invention and their homologues in specifictissues or developmental stages and the phenotypic performance acrossBarley accessions Corr. Corr. Gene P Exp. Set Gene P Exp. Set Name Rvalue set ID Name R value set ID LYD 0.71 4.80E 4 1 LYD 0.78 2.21E 4 1370 − 371 − 02 02 Provided are the correlations (R) between theexpression levels yield improving genes and their homologs in varioustissues [Expression (Exp) sets] and the phenotypic performance(Correlation vector (Corr.) ID)] under normal conditions across barleyvarieties. P = p value.

Example 11 Production of Cotton Transcriptom and High ThroughputCorrelation Analysis for Plant Fiber Development Using CottonOligonucleotide Microarray

In order to conduct high throughput gene expression correlationanalysis, the present inventors used cotton oligonucleotide microarray,designed and produced by “Comparative Evolutionary Genomics of Cotton”[Hypertext Transfer Protocol www (dot) cottonevolution (dot) info/).This Cotton Oligonucleotide Microarray is composed of 12,006 IntegratedDNA Technologies (IDT) oligonucleotides derived from an assembly of morethan 180,000 Gossypium ESTs sequenced from 30 cDNA libraries. Foradditional details see PCT/IL2005/000627 and PCT/IL2007/001590 which arefully incorporated herein by reference.

TABLE 49 Cotton transcriptom experimental sets Expression Set Set IDcotton fiber length 15 days post anthesis 1 cotton fiber length 5 dayspost anthesis 2 cotton fiber length 10 days post anthesis 3 Provided arethe cotton transcriptom expression sets.

In order to define correlations between the levels of RNA expression andfiber length, fibers from 8 different cotton lines were analyzed. Thesefibers were selected showing very good fiber quality and high lint index(Pima types, originating from other cotton species, namely G.barbadense), different levels of quality and lint indexes from variousG. hirsutum lines: good quality and high lint index (Acala type), andpoor quality and short lint index (Tamcot type, and old varieties). Asummary of the fiber length of the different lines is provided in Table51.

Experimental Procedures

RNA extraction—Fiber development stages, representing different fibercharacteristics, at 5, 10 and 15 DPA (Days After Anthesis) were sampledand RNA was extracted as described above.

Fiber length assessment—Fiber length of the selected cotton lines wasmeasured using fibrograph. The fibrograph system was used to computelength in terms of “Upper Half Mean” length. The upper half mean (UHM)is the average length of longer half of the fiber distribution. Thefibrograph measures length in span lengths at a given percentage pointWorld Wide Web (dot) cottoninc (dot)com/ClassificationofCotton/?Pg=4#Length].

Experimental Results

Eight different cotton lines were grown, and their fiber length wasmeasured. The fibers UHM values are summarized in Table 51 herein below.The correlation between expression level of genes of some embodiments ofthe invention and cotton fiber length under normal growth conditions wasperformed (Table 52).

TABLE 50 Cotton correlation parameter Correlated parameter withCorrelation ID Fiber Length 1

TABLE 51 Summary of the fiber length (UHM) of the 8 different cottonlines Correlation ID No./Ecotype 1 Line-1 1.21 Line-2 1.1 Line-3 1.36Line-4 1.26 Line-5 0.89 Line-6 1.01 Line-7 1.06 Line-8 1.15 Presentedare the UHM of 8 different cotton lines.

TABLE 52 Correlation between the expression level of selected LYD genesof some embodiments of the invention in various tissues and cotton fiberlength under normal growth conditions in cotton Corr. Corr. Gene Exp.Set Gene P Exp. Set Name R P value set ID Name R value set ID LYD 0.841.92E− 3 1 LYD 1.92E− 0.79 2 1 380 02 382 02 LYD 0.87 1.08E− 3 1 LYD4.20E− 0.72 1 1 382 02 383 02 LYD 0.77 2.52E− 1 1 LYD 2.70E− 0.76 2 1385 02 386 02 LYD 0.77 4.35E− 3 1 LYD 9.34E− 0.84 1 1 386 02 387 03 LYD0.88 9.63E− 3 1 LYD 6.19E− 0.73 3 1 388 03 502 02 Provided are thecorrelations between the expression level of the genes and the effect onfiber length. “Exp. Set” - Expression set. “R” = Pearson correlationcoefficient; “P” = p value.

Example 12 Identification of Genes which Increase Yield, Biomass, GrowthRate, Vigor, Oil Content, Abiotic Stress Tolerance of Plants andNitrogen Use Efficiency

Based on the above described bioinformatics and experimental tools, thepresent inventors have identified 201 genes which have a major impact onyield, seed yield, oil yield, biomass, growth rate, vigor, oil content,fiber yield, fiber quality, abiotic stress tolerance, and/or fertilizer(e.g., nitrogen) use efficiency when expression thereof is increased inplants. The identified genes (including genes identified bybioinformatics tools, variants, curated sequences thereof and clonedsequences), and polypeptide sequences encoded thereby are summarized inTable 53, hereinbelow.

TABLE 53 Identified polynucleotides which affect plant yield, seedyield, oil yield, oil content, biomass, growth rate, vigor, fiber yield,fiber quality abiotic stress tolerance and/or nitrogen use efficiency ofa plant Polyn. Polyp. Gene SEQ ID SEQ ID Name Cluster Name Organism NO:NO: LYD289 arabidopsis|10v1|AT1G02040 arabidopsis 1 456 LYD290arabidopsis|10v1|AT1G09560 arabidopsis 2 457 LYD291arabidopsis|10v1|AT1G10970 arabidopsis 3 458 LYD292arabidopsis|10v1|AT1G13740 arabidopsis 4 459 LYD293arabidopsis|10v1|ATIG14620 arabidopsis 5 460 LYD294arabidopsis|10v1|AT1G27300 arabidopsis 6 461 LYD295arabidopsis|10v1|AT1G27900 arabidopsis 7 462 LYD296arabidopsis|10v1|AT1G30820 arabidopsis 8 463 LYD297arabidopsis|10v1|AT1G51440 arabidopsis 9 464 LYD298arabidopsis|10v1|AT1G55910 arabidopsis 10 465 LYD299arabidopsis|10v1|AT1G61600 arabidopsis 11 466 LYD300arabidopsis|10v1|AT1G61790 arabidopsis 12 467 LYD301arabidopsis|10v1|ATIG74790 arabidopsis 13 468 LYD302arabidopsis|10v1|AT1G77060 arabidopsis 14 469 LYD303arabidopsis|10v1|AT2G01710 arabidopsis 15 470 LYD304arabidopsis|10v1|AT2G03810 arabidopsis 16 471 LYD305arabidopsis|10v1|AT2G05220 arabidopsis 17 472 LYD306arabidopsis|10v1|AT2G07674 arabidopsis 18 473 LYD307arabidopsis|10v1|AT2G17990 arabidopsis 19 474 LYD308arabidopsis|10v1|AT2G37478 arabidopsis 20 475 LYD309arabidopsis|10v1|AT2G40020 arabidopsis 21 476 LYD310arabidopsis|10v1|AT2G40300 arabidopsis 22 477 LYD311arabidopsis|10v1|AT2G40510 arabidopsis 23 478 LYD312arabidopsis|10v1|AT2G42770 arabidopsis 24 479 LYD313arabidopsis|10v1|AT3G04620 arabidopsis 25 480 LYD315arabidopsis|10v1|AT3G05390 arabidopsis 26 481 LYD316arabidopsis|10v1|AT3G09030 arabidopsis 27 482 LYD318arabidopsis|10v1|AT3G11900 arabidopsis 28 483 LYD319arabidopsis|10v1|AT3G14070 arabidopsis 29 484 LYD320arabidopsis|10v1|AT3G15810 arabidopsis 30 485 LYD321arabidopsis|10v1|AT3G18750 arabidopsis 31 486 LYD322arabidopsis|10v1|AT3G21190 arabidopsis 32 487 LYD323arabidopsis|10v1|AT3G44280 arabidopsis 33 488 LYD324arabidopsis|10v1|AT3G47860 arabidopsis 34 489 LYD325arabidopsis|10v1|AT3G49390 arabidopsis 35 490 LYD326arabidopsis|10v1|AT3G49490 arabidopsis 36 491 LYD327arabidopsis|10v1|AT3G51895 arabidopsis 37 492 LYD328arabidopsis|10v1|AT3G59210 arabidopsis 38 493 LYD329arabidopsis|10v1|AT3G62270 arabidopsis 39 494 LYD330arabidopsis|10v1|AT4G13070 arabidopsis 40 495 LYD331arabidopsis|10v1|AT4G17440 arabidopsis 41 496 LYD332arabidopsis|10v1|AT4G35110 arabidopsis 42 497 LYD334arabidopsis|10v1|AT5G03870 arabidopsis 43 498 LYD335arabidopsis|10v1|AT5G04140 arabidopsis 44 499 LYD337arabidopsis|10v1|AT5G11740 arabidopsis 45 500 LYD338arabidopsis|10v1|AT5G12410 arabidopsis 46 501 LYD339arabidopsis|10v1|AT5G13560 arabidopsis 47 502 LYD340arabidopsis|10v1|AT5G16420 arabidopsis 48 503 LYD341arabidopsis|10v1|AT5G36700 arabidopsis 49 504 LYD342arabidopsis|10v1|AT5G44680 arabidopsis 50 505 LYD343arabidopsis|10v1|AT5G46150 arabidopsis 51 506 LYD344arabidopsis|10v1|AT5G64840 arabidopsis 52 507 LYD346b_juncea|10v2|BJ1SLX00003156 b_juncea 53 508 LYD347b_juncea|10v2|BJ1SLX00219277D1 b_juncea 54 509 LYD348b_juncea|10v2|BJ1SLX01241733D1 b_juncea 55 510 LYD349b_juncea|10v2|E6ANDIZ01A0PVA b_juncea 56 511 LYD351b_juncea|10v2|E6ANDIZ01A2WXZ b_juncea 57 512 LYD352b_juncea|10v2|E6ANDIZ01A7124 b_juncea 58 513 LYD353b_juncea|10v2|E6ANDIZ01AK44C b_juncea 59 514 LYD354b_juncea|10v2|E6ANDIZ01ALST2 b_juncea 60 515 LYD355b_juncea|10v2|E6ANDIZ01AM1M7 b_juncea 61 516 LYD356b_juncea|10v2|E6ANDIZ01AR3Y3 b_juncea 62 517 LYD357b_juncea|10v2|E6ANDIZ01AU0CH b_juncea 63 518 LYD358b_juncea|10v2|E6ANDIZ01AUG5K b_juncea 64 519 LYD359b_juncea|10v2|E6ANDIZ01AVIGM b_juncea 65 520 LYD360b_juncea|10v2|E6ANDIZ01BHOKJ b_juncea 66 521 LYD361b_juncea|10v2|E6ANDIZ01BIDFA b_juncea 67 522 LYD362b_juncea|10v2|E6ANDIZ01C68KB b_juncea 68 523 LYD364b_juncea|10v2|E6ANDIZ01ET44E b_juncea 69 524 LYD365b_juncea|10v2|E6ANDIZ01EWUI0 b_juncea 70 525 LYD366b_juncea|10v2|E6ANDIZ02FS13L b_juncea 71 526 LYD367b_juncea|10v2|E6ANDIZ02GKPXS b_juncea 72 527 LYD368b_juncea|10v2|OXBJ1SLX00002741D1T1 b_juncea 73 528 LYD370barley|10v2|AV834829 barley 74 529 LYD371 barley|10v2|BJ450532 barley 75530 LYD372 canola|10v1|CD828626 canola 76 531 LYD375canola|10v1|DY011663 canola 77 532 LYD376 canola|10v1|ES964015 canola 78533 LYD377 canola|10v1|EV098360 canola 79 534 LYD378canola|10v1|EV114958 canola 80 535 LYD379 canola|10v1|EV129887 canola 81536 LYD380 cotton|10v1barbadense|BE054896 cotton 82 537 LYD381cotton|10v1|A1727565 cotton 83 538 LYD382 cotton|10v2|A1726887 cotton 84539 LYD383 cotton|10v2|BG447338 cotton 85 540 LYD385cotton|10v2|DN799940 cotton 86 541 LYD386 cotton|10v2|DN804420 cotton 87542 LYD387 cotton|10v2|DT466425 cotton 88 543 LYD388cotton|10v2|EX167553 cotton 89 544 LYD390 cotton|gb164|A1055341 cotton90 545 LYD391 maize|10v1|AA011869 maize 91 546 LYD392maize|10v1|BE512624 maize 92 547 LYD393 medicago|09v1|A1974481 medicago93 548 LYD395 medicago|09v1|AL379818 medicago 94 549 LYD396medicago|09v1|AW256719 medicago 95 550 LYD397 medicago|09v1|AW257291medicago 96 551 LYD398 medicago|09v1|AW329709 medicago 97 552 LYD399medicago|09v1|AW688882 medicago 98 553 LYD401 medicago|09v1|AW690536medicago 99 554 LYD402 medicago|09v1|AW694333 medicago 100 555 LYD403medicago|09v1|AW698677 medicago 101 556 LYD404 medicago|09v1|AW736500medicago 102 557 LYD405 medicago|09v1|AW775077 medicago 103 558 LYD407medicago|09v1|BE322971 medicago 104 559 LYD408 medicago|09v1|BE324051medicago 105 560 LYD409 medicago|09v1|BF521188 medicago 106 561 LYD410medicago|09v1|BG452469 medicago 107 562 LYD413 medicago|09v1|BQ124797medicago 108 563 LYD414 medicago|09v1|BQ157221 medicago 109 564 LYD415medicago|09v1|CX516971 medicago 110 565 LYD416 medicago|09v1|LLAJ388869medicago 111 566 LYD417 medicago|09v1|LLAL373168 medicago 112 567 LYD418medicago|09v1|LLAW688750 medicago 113 568 LYD419medicago|09v1|LLAW698759 medicago 114 569 LYD420medicago|09v1|LLAW776476 medicago 115 570 LYD421medicago|09v1|LLB1271813 medicago 116 571 LYD422medicago|09v1|MT454X026824 medicago 117 572 LYD423sorghum|09v1|SB01G027910 sorghum 118 573 LYD424 sorghum|09v1|SB01G046300sorghum 119 574 LYD425 sorghum|09v1|SB02G004290 sorghum 120 575 LYD427sorghum|09v1|SB03G025240 sorghum 121 576 LYD428 sorghum|09v1|SB04G002930sorghum 122 577 LYD431 sorghum|09v1|SB05G020810 sorghum 123 578 LYD432sorghum|09v1|SB06G021780 sorghum 124 579 LYD433 sorghum|09v1|SB07G014630sorghum 125 580 LYD434 sorghum|09v1|SB07G019310 sorghum 126 581 LYD435sorghum|09v1|SB07G019840 sorghum 127 582 LYD436 sorghum|09v1|SB09G003870sorghum 128 583 LYD437 soybean|11v1|GLYMA01G09460 soybean 129 584 LYD438soybean|11v1|GLYMA02G33320 soybean 130 585 LYD439soybean|11v1|GLYMA03G34340 soybean 131 586 LYD440soybean|11v1|GLYMA03G40870 soybean 132 587 LYD441soybean|11v1|GLYMA04G36500 soybean 133 588 LYD442soybean|11v1|GLYMA04G39480 soybean 134 589 LYD443soybean|11v1|GLYMA04G41020 soybean 135 590 LYD445soybean|11v1|GLYMA06G03510 soybean 136 591 LYD446soybean|11v1|GLYMA06G17910 soybean 137 592 LYD447soybean|11v1|GLYMA07G07150 soybean 138 593 LYD448soybean|11v1|GLYMA07G08010 soybean 139 594 LYD449soybean|11v1|GLYMA07G10060 soybean 140 595 LYD450soybean|11v1|GLYMA09G26770 soybean 141 596 LYD451soybean|11v1|GLYMA09G29610 soybean 142 597 LYD452soybean|11v1|GLYMA09G31720 soybean 143 598 LYD453soybean|11v1|GLYMA11G01120 soybean 144 599 LYD454soybean|11v1|GLYMA11G03570 soybean 145 600 LYD455soybean|11v1|GLYMA11G11560 soybean 146 601 LYD456soybean|11v1|GLYMA12G01770 soybean 147 602 LYD458soybean|11v1|GLYMA13G22110 soybean 148 603 LYD459soybean|11v1|GLYMA13G23920 soybean 149 604 LYD460soybean|11v1|GLYMA13G28620 soybean 150 605 LYD461soybean|11v1|GLYMA15G37980 soybean 151 606 LYD462soybean|11v1|GLYMA16G04350 soybean 152 607 LYD465soybean|11v1|GLYMA17G18250 soybean 153 608 LYD466soybean|11v1|GLYMA18G49340 soybean 154 609 LYD467soybean|11v1|GLYMA19G14700 soybean 155 610 LYD468soybean|11v1|GLYMA19G36240 soybean 156 611 LYD469soybean|11v1|GLYMA19G38830 soybean 157 612 LYD470soybean|11v1|GLYMA19G43610 soybean 158 613 LYD471soybean|11v1|GLYMA20G38820 soybean 159 614 LYD472 soybean|gb168|AW348492soybean 160 615 LYD473 soybean|gb168|BE661322 soybean 161 616 LYD474sunflower|10v1|CD849185 sunflower 162 617 LYD475 tomato|09v1|A1485596tomato 163 618 LYD477 tomato|09v1|BP884530 tomato 164 619 LYD478tomato|10v1|A1483112 tomato 165 620 LYD479 tomato|10v1|A1484249 tomato166 621 LYD480 tomato|10v1|A1771275 tomato 167 622 LYD481tomato|10v1|A1771986 tomato 168 623 LYD482 tomato|10v1|A1777950 tomato169 624 LYD483 tomato|10v1|AW738746 tomato 170 625 LYD484tomato|10v1|AW929870 tomato 171 626 LYD487 tomato|10v1|BG127385 tomato172 627 LYD489 tomato|10v1|BG131472 tomato 173 628 LYD491tomato|10v1|BM061560 tomato 174 629 LYD492 tomato|10v1|DB714406 tomato175 630 LYD495 wheat|gb164|BG604441 wheat 176 631 LYD497b_juncea|10v2|E6ANDIZ01AJCUK b_juncea 177 632 LYD498b_juncea|10v2|E6ANDIZ01AJQJC b_juncea 178 633 LYD499b_juncea|10v2|E6ANDIZ01B9PEA b_juncea 179 634 LYD500b_juncea|10v2|E6ANDIZ02FZU2Y2 b_juncea 180 635 LYD501b_juncea|10v2|E6ANDIZ02G70KP b_juncea 181 636 LYD502cotton|10v2|DW503396 cotton 182 637 LYD503 maize|10v1|AI637036 maize 183638 LYD504 medicago|09v1|AA660909 medicago 184 639 LYD505medicago|09v1|AJ388789 medicago 185 640 LYD506 medicago|09v1|BE239698medicago 186 641 LYD507 sorghum|09v1|SB01G017330 sorghum 187 642 LYD508sorghum|09v1|SB02G014460 sorghum 188 643 LYD509 sorghum|09v1|SB02G028300sorghum 189 644 LYD510 sorghum|09v1|SB09G025320 sorghum 190 645 LYD511soybean|11v1|BE660230 soybean 191 646 LYD512 soybean|11v1|GLYMA03G36420soybean 192 647 LYD513 soybean|11v1|GLYMA03G39480 soybean 193 648 LYD514soybean|11v1|GLYMA05G04990 soybean 194 649 LYD515soybean|11v1|GLYMA07G36970 soybean 195 650 LYD516soybean|11v1|GLYMA13G24040 soybean 196 651 LYD517soybean|11v1|GLYMA15G06930 soybean 197 652 LYD518soybean|11v1|GLYMA18G48880 soybean 198 653 LYD519 soybean|gb168|AW686841soybean 199 654 LYD520 soybean|gb168|FG994976 soybean 200 655 LYD496arabidopsis|10v1|AT1G58235 arabidopsis 201 — LYD299arabidopsis|10v1|AT1G61600 arabidopsis 202 466 LYD331arabidopsis|10v1|AT4G17440 arabidopsis 203 496 LYD340arabidopsis|10v1|AT5G16420 arabidopsis 204 503 LYD372canola|10v1|CD828626 canola 225 531 LYD379 canola|10v1|EV129887 canola229 536 LYD420 medicago|09v1|LLAW776476 medicago 237 570 LYD477tomato|09v1|BP884530 tomato 248 619 LYD479 tomato|10v1|A1484249 tomato249 621 LYD489 tomato|10v1|BG131472 tomato 251 628 LYD346b_juncea|10v2|BJ1SLX00003156 b_juncea 205 656 LYD347b_juncea|10v2|BJ1SLX00219277D1 b_juncea 206 657 LYD348b_juncea|10v2|BJ1SLX01241733D1 b_juncea 207 658 LYD349b_juncea|10v2|E6ANDIZ01A0PVA b_juncea 208 659 LYD351b_juncea|10v2|E6ANDIZ01A2WXZ b_juncea 209 660 LYD352b_juncea|10v2|E6ANDIZ01A7124 b_juncea 210 661 LYD353b_juncea|10v2|E6ANDIZ01AK44C b_juncea 211 662 LYD354b_juncea|10v2|E6ANDIZ01ALST2 b_juncea 212 663 LYD355b_juncea|10v2|E6ANDIZ01AM1M7 b_juncea 213 664 LYD356b_juncea|10v2|E6ANDIZ01AR3Y3 b_juncea 214 665 LYD357b_juncea|10v2|E6ANDIZ01AU0CH b_juncea 215 666 LYD358b_juncea|10v2|E6ANDIZ01AUG5K b_juncea 216 667 LYD359b_juncea|10v2|E6ANDIZ01AVIGM b_juncea 217 668 LYD360b_juncea|10v2|E6ANDIZ01BHOKJ b_juncea 218 669 LYD361b_juncea|10v2|E6ANDIZ01BIDFA b_juncea 219 670 LYD364b_juncea|10v2|E6ANDIZ01ET44E b_juncea 220 671 LYD365b_juncea|10v2|E6ANDIZ01EWUI0 b_juncea 221 672 LYD366b_juncea|10v2|E6ANDIZ02FS13L b_juncea 222 673 LYD367b_juncea|10v2|E6ANDIZ02GKPXS b_juncea 223 674 LYD371barley|10v2|BJ450532 barley 224 675 LYD376 canola|10v1|ES964015 canola226 676 LYD377 canola|10v1|EV098360 canola 227 677 LYD378canola|10v1|EV114958 canola 228 678 LYD380cotton|10v1barbadense|BE054896 cotton 230 679 LYD383cotton|10v2|BG447338 cotton 231 680 LYD388 cotton|10v2|EX167553 cotton232 681 LYD390 cotton|gb164|A1055341 cotton 233 682 LYD413medicago|09v1|BQ124797 medicago 234 683 LYD417 medicago|09v1|LLAL373168medicago 235 684 LYD418 medicago|09v1|LLAW688750 medicago 236 685 LYD421medicago|09v1|LLBI271813 medicago 238 686 LYD422medicago|09v1|MT454X026824 medicago 239 687 LYD431sorghum|09v1|SB05G020810 sorghum 240 688 LYD434 sorghum|09v1|SB07G019310sorghum 241 689 LYD443 soybean|11v1|GLYMA04G41020 soybean 242 690 LYD446soybean|11v1|GLYMA06G17910 soybean 243 691 LYD448soybean|11v1|GLYMA07G08010 soybean 244 692 LYD458soybean|11v1|GLYMA13G22110 soybean 245 693 LYD461soybean|11v1|GLYMA15G37980 soybean 246 694 LYD471soybean|11v1|GLYMA20G38820 soybean 247 695 LYD483 tomato|10v1|AW738746tomato 250 696 LYD495 wheat|gb164|BG604441 wheat 252 697 LYD497b_juncea|10v2|E6ANDIZ01AJCUK b_juncea 253 698 LYD499b_juncea|10v2|E6ANDIZ01B9PEA b_juncea 254 699 LYD500b_juncea|10v2|E6ANDIZ02FZU2Y2 b_juncea 255 700 LYD501b_juncea|10v2|E6ANDIZ02G70KP b_juncea 256 701 LYD514soybean|11v1|GLYMA05G04990 soybean 257 702 LYD496arabidopsis|10v1|AT1G58235 arabidopsis 258 — LYD289arabidopsis|10v1|AT1G02040 arabidopsis 259 456 LYD290arabidopsis|10v1|AT1G09560 arabidopsis 260 457 LYD291arabidopsis|10v1|AT1G10970 arabidopsis 261 458 LYD292arabidopsis|10v1|AT1G13740 arabidopsis 262 459 LYD293arabidopsis|10v1|AT1G14620 arabidopsis 263 460 LYD294arabidopsis|10v1|AT1G27300 arabidopsis 264 461 LYD295arabidopsis|10v1|AT1G27900 arabidopsis 265 462 LYD296arabidopsis|10v1|AT1G30820 arabidopsis 266 463 LYD298arabidopsis|10v1|AT1G55910 arabidopsis 268 465 LYD299arabidopsis|10v1|AT1G61600 arabidopsis 269 466 LYD300arabidopsis|10v1|AT1G61790 arabidopsis 270 467 LYD301arabidopsis|10v1|AT1G74790 arabidopsis 271 468 LYD302arabidopsis|10v1|AT1G77060 arabidopsis 272 469 LYD303arabidopsis|10v1|AT2G01710 arabidopsis 273 470 LYD304arabidopsis|10v1|AT2G03810 arabidopsis 274 471 LYD305arabidopsis|10v1|AT2G05220 arabidopsis 275 472 LYD307arabidopsis|10v1|AT2G17990 arabidopsis 277 474 LYD309arabidopsis|10v1|AT2G40020 arabidopsis 279 476 LYD311arabidopsis|10v1|AT2G40510 arabidopsis 281 478 LYD312arabidopsis|10v1|AT2G42770 arabidopsis 282 479 LYD313arabidopsis|10v1|AT3G04620 arabidopsis 283 480 LYD316arabidopsis|10v1|AT3G09030 arabidopsis 285 482 LYD318arabidopsis|10v1|AT3G11900 arabidopsis 286 483 LYD319arabidopsis|10v1|AT3G14070 arabidopsis 287 484 LYD320arabidopsis|10v1|AT3G15810 arabidopsis 288 485 LYD321arabidopsis|10v1|AT3G18750 arabidopsis 289 486 LYD322arabidopsis|10v1|AT3G21190 arabidopsis 290 487 LYD323arabidopsis|10v1|AT3G44280 arabidopsis 291 488 LYD324arabidopsis|10v1|AT3G47860 arabidopsis 292 489 LYD325arabidopsis|10v1|AT3G49390 arabidopsis 293 490 LYD326arabidopsis|10v1|AT3G49490 arabidopsis 294 491 LYD327arabidopsis|10v1|AT3G51895 arabidopsis 295 492 LYD328arabidopsis|10v1|AT3G59210 arabidopsis 296 493 LYD329arabidopsis|10v1|AT3G62270 arabidopsis 297 494 LYD330arabidopsis|10v1|AT4G13070 arabidopsis 298 495 LYD331arabidopsis|10v1|AT4G17440 arabidopsis 299 496 LYD332arabidopsis|10v1|AT4G35110 arabidopsis 300 497 LYD334arabidopsis|10v1|AT5G03870 arabidopsis 301 498 LYD335arabidopsis|10v1|AT5G04140 arabidopsis 302 499 LYD337arabidopsis|10v1|AT5G11740 arabidopsis 303 500 LYD338arabidopsis|10v1|AT5G12410 arabidopsis 304 501 LYD339arabidopsis|10v1|AT5G13560 arabidopsis 305 502 LYD340arabidopsis|10v1|AT5G16420 arabidopsis 306 503 LYD341arabidopsis|10v1|AT5G36700 arabidopsis 307 504 LYD342arabidopsis|10v1|AT5G44680 arabidopsis 308 505 LYD343arabidopsis|10v1|AT5G46150 arabidopsis 309 506 LYD344arabidopsis|10v1|AT5G64840 arabidopsis 310 507 LYD346b_juncea|10v2|BJ1SLX00003156 b_juncea 311 508 LYD355b_juncea|10v2|E6ANDIZ01AM1M7 b_juncea 319 516 LYD362b_juncea|10v2|E6ANDIZ01C68KB b_juncea 326 523 LYD368b_juncea|10v2|OXBJ1SLX00002741D1T1 b_juncea 331 528 LYD372canola|10v1|CD828626 canola 333 531 LYD376 canola|10v1|ES964015 canola335 533 LYD380 cotton|10v1barbadense|BE054896 cotton 339 537 LYD395medicago|09v1|AL379818 medicago 350 549 LYD399 medicago|09v1|AW688882medicago 354 553 LYD401 medicago|09v1|AW690536 medicago 355 554 LYD402medicago|09v1|AW694333 medicago 356 555 LYD407 medicago|09v1|BE322971medicago 360 559 LYD4I4 medicago|09v1|BQ157221 medicago 365 564 LYD423sorghum|09v1|SB01G027910 sorghum 373 573 LYD424 sorghum|09v1|SB01G046300sorghum 374 574 LYD425 sorghum|09v1|SB02G004290 sorghum 375 575 LYD427sorghum|09v1|SB03G025240 sorghum 376 576 LYD43I sorghum|09v1|SB05G020810sorghum 378 578 LYD432 sorghum|09v1|SB06G021780 sorghum 379 579 LYD433sorghum|09v1|SB07G014630 sorghum 380 580 LYD434 sorghum|09v1|SB07G019310sorghum 381 581 LYD435 sorghum|09v1|SB07G019840 sorghum 382 582 LYD437soybean|11v1|GLYMA01G09460 soybean 384 584 LYD438soybean|11v1|GLYMA02G33320 soybean 385 585 LYD439soybean|11v1|GLYMA03G34340 soybean 386 586 LYD440soybean|11v1|GLYMA03G40870 soybean 387 587 LYD44 1soybean|11v1|GLYMA04G36500 soybean 388 588 LYD442soybean|11v1|GLYMA04G39480 soybean 389 589 LYD443soybean|11v1|GLYMA04G41020 soybean 390 590 LYD445soybean|11v1|GLYMA06G03510 soybean 391 591 LYD448soybean|11v1|GLYMA07G08010 soybean 393 594 LYD450soybean|11v1|GLYMA09G26770 soybean 395 596 LYD451soybean|11v1|GLYMA09G29610 soybean 396 597 LYD453soybean|11v1|GLYMA11G01120 soybean 398 599 LYD454soybean|11v1|GLYMA11G03570 soybean 399 600 LYD458soybean|11v1|GLYMA13G22110 soybean 402 603 LYD459soybean|11v1|GLYMA13G23920 soybean 403 604 LYD460soybean|11v1|GLYMA13G28620 soybean 404 605 LYD461soybean|11v1|GLYMA15G37980 soybean 405 606 LYD465soybean|11v1|GLYMA17G18250 soybean 407 608 LYD466soybean|11v1|GLYMA18G49340 soybean 408 609 LYD467soybean|11v1|GLYMA19G14700 soybean 409 610 LYD468soybean|11v1|GLYMA19G36240 soybean 410 611 LYD469soybean|11v1|GLYMA19G38830 soybean 411 612 LYD471soybean|11v1|GLYMA20G38820 soybean 413 614 LYD472 soybean|gb168|AW348492soybean 414 615 LYD473 soybean|gb168|BE661322 soybean 415 616 LYD474sunflower|10v1|CD849185 sunflower 416 617 LYD475 tomato|09v1|A1485596tomato 417 618 LYD477 tomato|09v1|BP884530 tomato 418 619 LYD478tomato|10v1|A1483112 tomato 419 620 LYD479 tomato|10v1|A1484249 tomato420 621 LYD481 tomato|10v1|A1771986 tomato 422 623 LYD482tomato|10v1|A1777950 tomato 423 624 LYD484 tomato|10v1|AW929870 tomato425 626 LYD489 tomato|10v1|BG131472 tomato 427 628 LYD491tomato|10v1|BM061560 tomato 428 629 LYD492 tomato|10v1|DB714406 tomato429 630 LYD495 wheat|gb164|BG604441 wheat 430 631 LYD498b_juncea|10v2|E6ANDIZ01AJQJC b_juncea 432 633 LYD499b_juncea|10v2|E6ANDIZ01B9PEA b_juncea 433 634 LYD500b_juncea|10v2|E6ANDIZ02FZU2Y2 b_juncea 434 635 LYD503maize|10v1|A1637036 maize 437 638 LYD504 medicago|09v1|AA660909 medicago438 639 LYD506 medicago|09v1|BE239698 medicago 440 641 LYD507sorghum|09v1|SB01G017330 sorghum 441 642 LYD508 sorghum|09v1|SB02G014460sorghum 442 643 LYD509 sorghum|09v1|SB02G028300 sorghum 443 644 LYD510sorghum|09v1|SB09G025320 sorghum 444 645 LYD511 soybean|11v1|BE660230soybean 445 646 LYD512 soybean|11v1|GLYMA03G36420 soybean 446 647 LYD513soybean|11v1|GLYMA03G39480 soybean 447 648 LYD514soybean|11v1|GLYMA05G04990 soybean 448 649 LYD515soybean|11v1|GLYMA07G36970 soybean 449 650 LYD516soybean|11v1|GLYMA13G24040 soybean 450 651 LYD517soybean|11v1|GLYMA15G06930 soybean 451 652 LYD519 soybean|gb168|AW686841soybean 453 654 LYD297 arabidopsis|10v1|AT1G51440 arabidopsis 267 703LYD306 arabidopsis|10v1|AT2G07674 arabidopsis 276 704 LYD308arabidopsis|10v1|AT2G37478 arabidopsis 278 705 LYD310arabidopsis|10v1|AT2G40300 arabidopsis 280 706 LYD315arabidopsis|10v1|AT3G05390 arabidopsis 284 707 LYD347b_juncea|10v2|BJ1SLX00219277D1 b_juncea 312 708 LYD348b_juncea|10v2|BJ1SLX01241733D1 b_juncea 313 709 LYD349b_juncea|10v2|E6ANDIZ01A0PVA b_juncea 314 710 LYD351b_juncea|10v2|E6ANDIZ01A2WXZ b_juncea 315 711 LYD352b_juncea|10v2|E6ANDIZ01A7124 b_juncea 316 712 LYD353b_juncea|10v2|E6ANDIZ01AK44C b_juncea 317 713 LYD354b_juncea|10v2|E6ANDIZ01ALST2 b_juncea 318 714 LYD356b_juncea|10v2|E6ANDIZ01AR3Y3 b_juncea 320 715 LYD357b_juncea|10v2|E6ANDIZ01AU0CH b_juncea 321 716 LYD358b_juncea|10v2|E6ANDIZ01AUG5K b_juncea 322 717 LYD359b_juncea|10v2|E6ANDIZ01AVIGM b_juncea 323 718 LYD360b_juncea|10v2|E6ANDIZ01BHOKJ b_juncea 324 719 LYD361b_juncea|10v2|E6ANDIZ01BIDFA b_juncea 325 720 LYD364b_juncea|10v2|E6ANDIZ01ET44E b_juncea 327 721 LYD365b_juncea|10v2|E6ANDIZ01EWUI0 b_juncea 328 722 LYD366b_juncea|10v2|E6ANDIZ02FS13L b_juncea 329 723 LYD367b_juncea|10v2|E6ANDIZ02GKPXS b_juncea 330 724 LYD370barley|10v2|AV834829 barley 332 725 LYD375 canola|10v1|DY011663 canola334 726 LYD377 canola|10v1|EV098360 canola 336 727 LYD378canola|10v1|EV114958 canola 337 728 LYD379 canola|10v1|EV129887 canola338 729 LYD382 cotton|10v2|A1726887 cotton 340 730 LYD383cotton|10v2|BG447338 cotton 341 731 LYD385 cotton|10v2|DN799940 cotton342 732 LYD386 cotton|10v2|DN804420 cotton 343 733 LYD387cotton|10v2|DT466425 cotton 344 734 LYD388 cotton|10v2|EX167553 cotton345 735 LYD390 cotton|gb164|A1055341 cotton 346 736 LYD391maize|10v1|AA011869 maize 347 737 LYD392 maize|10v1|BE512624 maize 348738 LYD393 medicago|09v1|A1974481 medicago 349 739 LYD396medicago|09v1|AW256719 medicago 351 740 LYD397 medicago|09v1|AW257291medicago 352 741 LYD398 medicago|09v1|AW329709 medicago 353 742 LYD403medicago|09v1|AW698677 medicago 357 743 LYD404 medicago|09v1|AW736500medicago 358 744 LYD405 medicago|09v1|AW775077 medicago 359 745 LYD408medicago|09v1|BE324051 medicago 361 746 LYD409 medicago|09v1|BF521188medicago 362 747 LYD410 medicago|09v1|BG452469 medicago 363 748 LYD413medicago|09v1|BQ124797 medicago 364 749 LYD415 medicago|09v1|CX516971medicago 366 750 LYD4 16 medicago|09v1|LLAJ388869 medicago 367 751LYD417 medicago|09v1|LLAL373168 medicago 368 752 LYD418medicago|09v1|LLAW688750 medicago 369 753 LYD419medicago|09v1|LLAW698759 medicago 370 754 LYD420medicago|09v1|LLAW776476 medicago 371 755 LYD422medicago|09v1|MT454X026824 medicago 372 756 LYD428sorghum|09v1|SB04G002930 sorghum 377 757 LYD436 sorghum|09v1|SB09G003870sorghum 383 758 LYD446 soybean|11v1|GLYMA06G17910 soybean 392 759 LYD449soybean|11v1|GLYMA07G10060 soybean 394 760 LYD452soybean|11v1|GLYMA09G31720 soybean 397 761 LYD455soybean|11v1|GLYMA11G11560 soybean 400 762 LYD456soybean|11v1|GLYMA12G01770 soybean 401 763 LYD462soybean|11v1|GLYMA16G04350 soybean 406 764 LYD470soybean|11v1|GLYMA19G43610 soybean 412 765 LYD480 tomato|10v1|A1771275tomato 421 766 LYD483 tomato|10v1|AW738746 tomato 424 767 LYD487tomato|10v1|BG127385 tomato 426 768 LYD497 b_juncea|10v2|E6ANDIZ01AJCUKb_juncea 431 769 LYD501 b_juncea|10v2|E6ANDIZ02G70KP b_juncea 435 770LYD502 cotton|10v2|DW503396 cotton 436 771 LYD505 medicago|09v1|AJ388789medicago 439 772 LYD518 soybean|11v1|GLYMA18G48880 soybean 452 773LYD520 soybean|gb168|FG994976 soybean 454 774 LYD496arabidopsis|10v1|AT1G58235 arabidopsis 455 — Provided are the identifiedgenes, their annotation, organism and polynucleotide and polypeptidesequence identifiers. “polynucl.” = polynucleotide; “polypep.” =polypeptide.

Example 13 Identification of Homologous Sequences that Increase SeedYield, Oil Yield, Growth Rate, Oil Content, Fiber Yield, Fiber Quality,Biomass, Vigor, ABST and/or NUE of a Plant

The concepts of orthology and paralogy have recently been applied tofunctional characterizations and classifications on the scale ofwhole-genome comparisons. Orthologs and paralogs constitute two majortypes of homologs: The first evolved from a common ancestor byspecialization, and the latter are related by duplication events. It isassumed that paralogs arising from ancient duplication events are likelyto have diverged in function while true orthologs are more likely toretain identical function over evolutionary time.

To identify putative orthologs of the genes affecting plant yield, oilyield, oil content, seed yield, growth rate, vigor, biomass, abioticstress tolerance and/or nitrogen use efficiency, all sequences werealigned using the BLAST® (Basic Local Alignment Search Tool). Sequencessufficiently similar were tentatively grouped. These putative orthologswere further organized under a Phylogram—a branching diagram (tree)assumed to be a representation of the evolutionary relationships amongthe biological taxa. Putative ortholog groups were analyzed as to theiragreement with the phylogram and in cases of disagreements theseortholog groups were broken accordingly.

Expression data was analyzed and the EST libraries were classified usinga fixed vocabulary of custom terms such as developmental stages (e.g.,genes showing similar expression profile through development with upregulation at specific stage, such as at the seed filling stage) and/orplant organ (e.g., genes showing similar expression profile across theirorgans with up regulation at specific organs such as seed). Theannotations from all the ESTs clustered to a gene were analyzedstatistically by comparing their frequency in the cluster versus theirabundance in the database, allowing the construction of a numeric andgraphic expression profile of that gene, which is termed “digitalexpression”. The rationale of using these two complementary methods withmethods of phenotypic association studies of QTLs, SNPs and phenotypeexpression correlation is based on the assumption that true orthologsare likely to retain identical function over evolutionary time. Thesemethods provide different sets of indications on function similaritiesbetween two homologous genes, similarities in the sequencelevel—identical amino acids in the protein domains and similarity inexpression profiles.

The search and identification of homologous genes involves the screeningof sequence information available, for example, in public databases suchas the DNA Database of Japan (DDBJ), Genbank, and the European MolecularBiology Laboratory Nucleic Acid Sequence Database (EMBL) or versionsthereof or the MIPS database. A number of different search algorithmshave been developed, including but not limited to the suite of programsreferred to as BLAST® programs. There are five implementations ofBLAST®, three designed for nucleotide sequence queries (BLASTN, BLASTX,and TBLASTX) and two designed for protein sequence queries (BLASTP andTBLASTN) (Coulson, Trends in Biotechnology: 76-80, 1994; Birren et al.,Genome Analysis, I: 543, 1997). Such methods involve alignment andcomparison of sequences. The BLAST® algorithm calculates percentsequence identity and performs a statistical analysis of the similaritybetween the two sequences. The software for performing BLAST® analysisis publicly available through the National Centre for BiotechnologyInformation. Other such software or algorithms are GAP, BESTFIT, FASTAand TFASTA. GAP uses the algorithm of Needleman and Wunsch (J. Mol.Biol. 48: 443-453, 1970) to find the alignment of two complete sequencesthat maximizes the number of matches and minimizes the number of gaps.

The homologous genes may belong to the same gene family. The analysis ofa gene family may be carried out using sequence similarity analysis. Toperform this analysis one may use standard programs for multiplealignments e.g. Clustal W. A neighbour-joining tree of the proteinshomologous to the genes in this invention may be used to provide anoverview of structural and ancestral relationships. Sequence identitymay be calculated using an alignment program as described above. It isexpected that other plants will carry a similar functional gene(ortholog) or a family of similar genes and those genes will provide thesame preferred phenotype as the genes presented here. Advantageously,these family members may be useful in the methods of the invention.Example of other plants are included here but not limited to, barley(Hordeum vulgare), Arabidopsis (Arabidopsis thaliana), maize (Zea mays),cotton (Gossypium), Oilseed rape (Brassica napus), Rice (Oryza sativa),Sugar cane (Saccharum officinarum), Sorghum (Sorghum bicolor), Soybean(Glycine max), Sunflower (Helianthus annuus), Tomato (Lycopersiconesculentum), Wheat (Triticum aestivum).

The above-mentioned analyses for sequence homology can be carried out ona full-length sequence, but may also be based on a comparison of certainregions such as conserved domains. The identification of such domains,would also be well within the realm of the person skilled in the art andwould involve, for example, a computer readable format of the nucleicacids of the present invention, the use of alignment software programsand the use of publicly available information on protein domains,conserved motifs and boxes. This information is available in the PRODOM(Hypertext Transfer Protocol://World Wide Web (dot) biochem (dot) ucl(dot) ac (dot) uk/bsm/dbbrowser/protocol/prodomqry (dot) html), PIR(Hypertext Transfer Protocol://pir (dot) Georgetown (dot) edu/) or Pfam(Hypertext Transfer Protocol://World Wide Web (dot) sanger (dot) ac(dot) uk/Software/Pfam/) database. Sequence analysis programs designedfor motif searching may be used for identification of fragments, regionsand conserved domains as mentioned above. Preferred computer programsinclude, but are not limited to, MEME, SIGNALSCAN, and GENESCAN.

A person skilled in the art may use the homologous sequences providedherein to find similar sequences in other species and other organisms.Homologues of a protein encompass, peptides, oligopeptides,polypeptides, proteins and enzymes having amino acid substitutions,deletions and/or insertions relative to the unmodified protein inquestion and having similar biological and functional activity as theunmodified protein from which they are derived. To produce suchhomologues, amino acids of the protein may be replaced by other aminoacids having similar properties (conservative changes, such as similarhydrophobicity, hydrophilicity, antigenicity, propensity to form orbreak a-helical structures or 3-sheet structures). Conservativesubstitution tables are well known in the art (see for example Creighton(1984) Proteins. W.H. Freeman and Company). Homologues of a nucleic acidencompass nucleic acids having nucleotide substitutions, deletionsand/or insertions relative to the unmodified nucleic acid in questionand having similar biological and functional activity as the unmodifiednucleic acid from which they are derived.

Table 54, hereinbelow, lists a summary of orthologous and homologoussequences of the polynucleotide sequences and polypeptide sequencespresented in Table 53 above, which were identified from the databasesusing the NCBI BLAST® software (e.g., using the Blastp and tBlastnalgorithms) and needle (EMBOSS package) as being at least 80% homologousto the selected polynucleotides and polypeptides, and which are expectedto increase plant yield, seed yield, oil yield, oil content, growthrate, fiber yield, fiber quality, biomass, vigor, ABST and/or NUE of aplant.

Lengthy table referenced here US20210371872A1-20211202-T00001 Pleaserefer to the end of the specification for access instructions.

Example 14 Gene Cloning and Generation of Binary Vectors for PlantExpression

To validate their role in improving oil content, plant yield, seedyield, oil content, biomass, growth rate, fiber yield, fiber quality,ABST, NUE and/or vigor, selected genes were over-expressed in plants, asfollows.

Cloning Strategy

Selected genes from those listed in Examples 12 and 13 hereinabove werecloned into binary vectors for the generation of transgenic plants. Forcloning, the full-length open reading frame (ORF) was first identified.In case of ORF-EST clusters and in some cases already published mRNAsequences were analyzed to identify the entire open reading frame bycomparing the results of several translation algorithms to knownproteins from other plant species. To clone the full-length cDNAs,reverse transcription (RT) followed by polymerase chain reaction (PCR;RT-PCR) was performed on total RNA extracted from leaves, flowers,siliques or other plant tissues, growing under normal and differenttreated conditions. Total RNA was extracted as described in “GENERALEXPERIMENTAL AND BIOINFORMATICS METHODS” above. Production of cDNA andPCR amplification was performed using standard protocols describedelsewhere (Sambrook J., E. F. Fritsch. and T. Maniatis. 1989. MolecularCloning. A Laboratory Manual., 2nd Ed. Cold Spring Harbor LaboratoryPress, New York) which are well known to those skilled in the art. PCRproducts are purified using PCR purification kit (Qiagen). In case wherethe entire coding sequence was not found, RACE kit from Invitrogen(RACE=R apid A mplification of cDNA E nds) was used to access the fullcDNA transcript of the gene from the RNA samples described above. RACEproducts were cloned into high copy vector followed by sequencing ordirectly sequenced.

The information from the RACE procedure was used for cloning of the fulllength ORF of the corresponding genes.

In case genomic DNA is cloned, the genes were amplified by direct PCR ongenomic DNA extracted from leaf tissue using the DNAeasy kit (QiagenCat. No. 69104).

Usually, 2 sets of primers were synthesized for the amplification ofeach gene from a cDNA or a genomic sequence; an external set of primersand an internal set (nested PCR primers). When needed (e.g., when thefirst PCR reaction does not result in a satisfactory product forsequencing), an additional primer (or two) of the nested PCR primers wasused.

To facilitate cloning of the cDNAs/genomic sequences, a 8-12 bpextension was added to the 5′ of each primer. The primer extensionincludes an endonuclease restriction site. The restriction sites wereselected using two parameters: (a). The site does not exist in the cDNAsequence; and (b). The restriction sites in the forward and reverseprimers are designed such that the digested cDNA is inserted in thesense formation into the binary vector utilized for transformation.

Each digested PCR product was inserted into a high copy vector pUC19(New England BioLabs Inc], or into plasmids originating from thisvector. In some cases the undigested PCR product was inserted intopCR-Blunt II-TOPO (Invitrogen).

Sequencing of the amplified PCR products was performed, using ABI 377sequencer (Amersham Biosciences Inc). In some cases, after confirmingthe sequences of the cloned genes, the cloned cDNA was introduced into amodified pGI binary vector containing the At6669 promoter via digestionwith appropriate restriction endonucleases. In any case the insert wasfollowed by single copy of the NOS terminator (SEQ ID NO: 14481). Thedigested products and the linearized plasmid 3n vector were ligatedusing T4 DNA ligase enzyme (Roche, Switzerland).

High copy plasmids containing the cloned genes were digested with therestriction endonucleases (New England BioLabs Inc) according to thesites designed in the primers and cloned into binary vectors.

Several DNA sequences of the selected genes were synthesized by acommercial supplier GeneArt [Hypertext Transfer Protocol://World WideWeb (dot) geneart (dot) com/]. Synthetic DNA was designed in silico.Suitable restriction enzymes sites were added to the cloned sequences atthe 5′ end and at the 3′ end to enable later cloning into the pQFNcbinary vector downstream of the At6669 promoter (SEQ ID NO: 14467).

Binary vectors used for cloning: The plasmid pPI was constructed byinserting a synthetic poly-(A) signal sequence, originating from pGL3basic plasmid vector (Promega, Acc No U47295; bp 4658-4811) into theHindIII restriction site of the binary vector pBI101.3 (Clontech, Acc.No. U12640). pGI (pBXYN) is similar to pPI, but the original gene in thebackbone, the GUS gene, is replaced by the GUS-Intron gene followed bythe NOS terminator (SEQ ID NO: 14481) (Vancanneyt. G, et al MGG 220,245-50, 1990). pGI was used in the past to clone the polynucleotidesequences, initially under the control of 35S promoter [Odell, J T, etal. Nature 313, 810-812 (28 Feb. 1985); SEQ ID NO: 14465].

The modified pGI vectors [pQXNc (FIG. 8); or pQFN (FIG. 2), pQFNc (FIG.2) or pQYN 6669 (FIG. 1)] are modified versions of the pGI vector inwhich the cassette is inverted between the left and right borders so thegene and its corresponding promoter are close to the right border andthe NPTII gene is close to the left border.

At6669, the Arabidopsis thaliana promoter sequence (SEQ ID NO:14467) wasinserted in the modified pGI binary vector, upstream to the clonedgenes, followed by DNA ligation and binary plasmid extraction frompositive E. coli colonies, as described above.

Colonies were analyzed by PCR using the primers covering the insertwhich are designed to span the introduced promoter and gene. Positiveplasmids were identified, isolated and sequenced.

Selected genes cloned by the present inventors are provided in Table 55below.

TABLE 55 Genes cloned in High copy number plasmids Polyn. Polyp. GenePrimers used SEQ ID SEQ ID Name High copy plasmid Organism SEQ ID NOs:NO: NO: LYD289 pUC19c_LYD289 Arabidopsis thalia 14482, 14670, 14482,14670 259 456 LYD290 pUC19c_LYD290 Arabidopsis thalia 14483, 14671 260457 LYD291 pUC19c_LYD291 Arabidopsis thalia 14484, 14672 261 458 LYD292pUC19c_LYD292 Arabidopsis thalia 14485, 14673, 14858, 14955 262 459LYD293 pUC19c_LYD293 Arabidopsis thalia 14486, 14674, 14859, 14956 263460 LYD294 pUC19c_LYD294 Arabidopsis thalia 14487, 14675, 14860, 14957264 461 LYD295 pUC19c_LYD295 Arabidopsis thalia 14488, 14676, 14488,14676 265 462 LYD296 pUC19c_LYD296 Arabidopsis thalia 14489, 14677,14861, 14958 266 463 LYD297 pUC19c_LYD297 Arabidopsis thalia 14490,14678, 14862, 14678 267 703 LYD298 pUC19c_LYD298 Arabidopsis thalia14491, 14679, 14863, 14959 268 465 LYD299 pMA_LYD299_GA GeneArt 269 466LYD300 pOA_LYD300_GA GeneArt 270 467 LYD301 pUC19d_LYD301 Arabidopsisthalia 14492, 14680, 14864, 14960 271 468 LYD302 pUC19c_LYD302Arabidopsis thalia 14493, 14681, 14493, 14961 272 469 LYD303pUC19c_LYD303 Arabidopsis thalia 14494, 14682, 14865, 14962 273 470LYD304 pUC19c_LYD304 Arabidopsis thalia 14495, 14683, 14495, 14683 274471 LYD305 pUC19c_LYD305 Arabidopsis thalia 14496, 14684, 14866, 14963275 472 LYD306 pUC19c_LYD306 Arabidopsis thalia 14497, 14685 276 704LYD307 pUC19c_LYD307 Arabidopsis thalia 14498, 14686, 14867, 14964 277474 LYD308 pUC19c_LYD308 Arabidopsis thalia 14499, 14687, 14868, 14965278 705 LYD309 pUC19c_LYD309 Arabidopsis thalia 14500, 14688, 14500,14966 279 476 LYD310 pUC19c_LYD310 Arabidopsis thalia 14501, 14689,14501, 14689 280 706 LYD311 pUC19c_LYD311 Arabidopsis thalia 14502,14690, 14502, 14690 281 478 LYD312 pUC19c_LYD312 Arabidopsis thalia14503, 14691, 14503, 14691 282 479 LYD313 pUC19c_LYD313 Arabidopsisthalia 14504, 14692, 14504, 14692 283 480 LYD315 pUC19c_LYD315Arabidopsis thalia 14505, 14693, 14869, 14967 284 707 LYD316pUC19c_LYD316 Arabidopsis thalia 14506, 14694, 14506, 14694 285 482LYD318 pUC19c_LYD318 Arabidopsis thalia 14507, 14695, 14870, 14968 286483 LYD319 pUC19c_LYD319 Arabidopsis thalia 14508, 14696, 14871, 14696287 484 LYD320 pUC19c_LYD320 Arabidopsis thalia 14509, 14697, 14872,14969 288 485 LYD321 pUC19c_LYD321 Arabidopsis thalia 14510, 14698,14873, 14970 289 486 LYD322 pUC19c_LYD322 Arabidopsis thalia 14511,14699, 14874, 14971 290 487 LYD323 pUC19c_LYD323 Arabidopsis thalia14512, 14700, 14875, 14972 291 488 LYD324 pUC19c_LYD324 Arabidopsisthalia 14513, 14701 292 489 LYD325 pUC19c_LYD325 Arabidopsis thalia14514, 14702, 14514, 14702 293 490 LYD326 pUC19c_LYD326 Arabidopsisthalia 14515, 14703 294 491 LYD327 TopoB_LYD327 Arabidopsis thalia14516, 14704, 14877, 14974 295 492 LYD328 pUC19c_LYD328 Arabidopsisthalia 14517, 14705, 14878, 14975 296 493 LYD329 pUC19c_LYD329Arabidopsis thalia 14518, 14706, 14879, 14976 297 494 LYD330pUC19c_LYD330 Arabidopsis thalia 14519, 14707, 14880, 14977 298 495LYD331 pUC19c_LYD331 Arabidopsis thalia 14520, 14708, 14881, 14978 299496 LYD332 pUC19c_LYD332 Arabidopsis thalia 14521, 14709, 14882, 14979300 497 LYD334 pUC19c_LYD334 Arabidopsis thalia 14522, 14710, 14522,14980 301 498 LYD335 pUC19c_LYD335 Arabidopsis thalia 14523, 14711,14883, 14981 302 499 LYD337 pUC19c_LYD337 Arabidopsis thalia 14524,14712 303 500 LYD338 pUC19c_LYD338 Arabidopsis thalia 14525, 14713,14525, 14982 304 501 LYD339 pUC19c_LYD339 Arabidopsis thalia 14526,14714, 14884, 14983 305 502 LYD340 pUC19c_LYD340 Arabidopsis thalia14527, 14715, 14527, 14715 306 503 LYD341 pUC19c_LYD341 Arabidopsisthalia 14528, 14716, 14885, 14984 307 504 LYD342 pUC19c_LYD342Arabidopsis thalia 14529, 14717, 14886, 14985 308 505 LYD343pUC19c_LYD343 Arabidopsis thalia 14530, 14718, 14887, 14986 309 506LYD344 pUC19c_LYD344 Arabidopsis thalia 14531, 14719, 14531, 14719 310507 LYD346 pUC19c_LYD346 Brassica juncea 14532, 14720, 14532, 14720 311508 LYD347 pUC19c_LYD347 Brassica juncea 14533, 14721, 14888, 14721 312708 LYD348 pUC19c_LYD348 Brassica juncea 14534, 14722, 14889, 14987 313709 LYD349 pUC19c_LYD349 Brassica juncea 14535, 14723, 14535, 14723 314710 LYD351 pUC19c_LYD351 Brassica juncea 14536, 14724, 14890, 14988 315711 LYD352 pUC19_LYD352 Brassica juncea 14537, 14725, 14537, 14725 316712 LYD353 pUC19c_LYD353 Brassica juncea 14538, 14726, 14538, 14726 317713 LYD354 pUC19_LYD354 Brassica juncea 14539, 14727, 14539, 14727 318714 LYD355 pUC19c_LYD355 Brassica juncea 14540, 14728, 14540, 14728 319516 LYD356 pUC19c_LYD356 Brassica juncea 14541, 14729, 14541, 14729 320715 LYD357 pUC19c_LYD357 Brassica juncea 14542, 14730, 14891, 14989 321716 LYD358 pUC19_LYD358 Brassica juncea 14543, 14731, 14892, 14990 322717 LYD359 pUC19c_LYD359 Brassica juncea 14544, 14732, 14544, 14991 323718 LYD360 pUC19c_LYD360 Brassica juncea 14545, 14733, 14545, 14733 324719 LYD361 pUC19c_LYD361 Brassica juncea 14546, 14734, 14546, 14734 325720 LYD362 pUC19c_LYD362 Brassica juncea 14547, 14735, 14893, 14992 326523 LYD364 pUC19_LYD364 Brassica juncea 14548, 14736, 14894, 14736 327721 LYD365 pUC19c_LYD365 Brassica juncea 14549, 14737 328 722 LYD366pUC19c_LYD366 Brassica juncea 14550, 14738, 14895, 14993 329 723 LYD367pUC19c_LYD367 Brassica juncea 14551, 14739, 14551, 14739 330 724 LYD368pUC19c_LYD368 Brassica juncea 14552, 14740, 14552, 14994 331 528 LYD370pUC19c_LYD370 BARLEY Hordeum vulgare L. 14553, 14741, 14553, 14741 332725 LYD372 pUC19d_LYD372 CANOLA Brassica napus 14554, 14742, 14896,14995 333 531 LYD375 pUC19c_LYD375 CANOLA Brassica napus 14555, 14743,14555, 14996 334 726 LYD376 pUC19c_LYD376 CANOLA Brassica napus 14556,14744, 14897, 14997 335 533 LYD377 TopoB_LYD377 CANOLA Brassica napus14557, 14745, 14898, 14998 336 727 LYD378 pUC19c_LYD378 CANOLA Brassicanapus 14558, 14746, 14558, 14746 337 728 LYD379 pUC19c_LYD379 CANOLABrassica napus 14559, 14747 338 729 LYD380 pMK-RQ_LYD380_GA GeneArt 339537 LYD382 pUC19c_LYD382 COTTON Gossypium barbadense 14560, 14748,14560, 14748 340 730 LYD383 pQFNc_LYD383 COTTON Gossypium hirsutum14561, 14749, 14899, 14999 341 731 LYD385 pUC19c_LYD385 COTTON Gossypiumbarbadense 14562, 14750, 14900, 15000 342 732 LYD386 pUC19c_LYD386COTTON Gossypium barbadense 14563, 14751, 14901, 15001 343 733 LYD387pUC19c_LYD387 COTTON Gossypium barbadense 14564, 14752, 14902, 15002 344734 LYD388 pUC19c_LYD388 COTTON Gossypium barbadense 14565, 14753,14565, 14753 345 735 LYD390 pUC19c_LYD390 COTTON Gossypium barbadense14566, 14754 346 736 LYD391 pUC19_LYD391 MAIZE Zea mays L. 14567, 14755,14567, 14755 347 737 LYD392 pUC19c_LYD392 MAIZE Zea mays L. 14568,14756, 14904, 15004 348 738 LYD393 pUC19c_LYD393 MEDICAGO Medicagotrancatula 14569, 14757, 14569, 15005 349 739 LYD395 pUC19c_LYD395MEDICAGO Medicago trancatula 14570, 14758, 14905, 15006 350 549 LYD396pUC19c_LYD396 MEDICAGO Medicago trancatula 14571, 14759, 14906, 15007351 740 LYD397 pUC19c_LYD397 MEDICAGO Medicago trancatula 14572, 14760,14907, 15008 352 741 LYD398 pUC19c_LYD398 MEDICAGO Medicago trancatula14573, 14761, 14573, 14761 353 742 LYD399 pUC19c_LYD399 MEDICAGOMedicago trancatula 14574, 14762, 14908, 15009 354 553 LYD401pUC19c_LYD401 MEDICAGO Medicago trancatula 14575, 14763, 14909, 15010355 554 LYD402 pUC19c_LYD402 MEDICAGO Medicago trancatula 14576, 14764,14910, 15011 356 555 LYD403 pUC19c_LYD403 MEDICAGO Medicago trancatula14577, 14765, 14911, 15012 357 743 LYD404 pUC19c_LYD404 MEDICAGOMedicago trancatula 14578, 14766, 14578, 15013 358 744 LYD405pUC19c_LYD405 MEDICAGO Medicago trancatula 14579, 14767, 14579, 15014359 745 LYD407 pMK-RQ_LYD407_GA GeneArt 360 559 LYD408 pUC19c_LYD408MEDICAGO Medicago trancatula 14580, 14768, 14580, 15015 361 746 LYD409pUC19c_LYD409 MEDICAGO Medicago trancatula 14581, 14769, 14912, 15016362 747 LYD410 pUC19c_LYD410 MEDICAGO Medicago trancatula 14582, 14770,14913, 15017 363 748 LYD413 pUC19d_LYD413 MEDICAGO Medicago trancatula14583, 14771, 14914, 14771 364 749 LYD414 pUC19c_LYD414 MEDICAGOMedicago trancatula 14584, 14772, 14915, 15018 365 564 LYD415pUC19c_LYD415 MEDICAGO Medicago trancatula 14585, 14773, 14916, 15019366 750 LYD416 pUC19c_LYD416 MEDICAGO Medicago trancatula 14586, 14774,14586, 14774 367 751 LYD417 pUC19c_LYD417 MEDICAGO Medicago trancatula14587, 14775, 14587, 15020 368 752 LYD418 pUC19c_LYD418 MEDICAGOMedicago trancatula 14588, 14776, 14588, 14776 369 753 LYD419pUC19c_LYD419 MEDICAGO Medicago trancatula 14589, 14777, 14917, 15021370 754 LYD420 pUC19c_LYD420 MEDICAGO Medicago trancatula 14590, 14778,14590, 14778 371 755 LYD422 pUC19c_LYD422 MEDICAGO Medicago trancatula14591, 14779, 14918, 14779 372 756 LYD423 pUC19c_LYD423 Sorghum bicolor14592, 14780, 14592, 15022 373 573 LYD424 pUC19c_LYD424 Sorghum bicolor14593, 14781, 14593, 14781 374 574 LYD425 pUC19c_LYD425 Sorghum bicolor14594, 14782, 14919, 15023 375 575 LYD427 pMA-RQ_LYD427_GA GeneArt 376576 LYD428 pUC19c_LYD428 Sorghum bicolor 14595, 14783, 14595, 15024 377757 LYD431 pMA_LYD431_GA GeneArt 378 578 LYD432 pUC19c_LYD432 Sorghumbicolor 14596, 14784, 14920, 15025 379 579 LYD433 TopoB_LYD433 Sorghumbicolor 14597, 14785, 14597, 14785 380 580 LYD434 pUC19c_LYD434 Sorghumbicolor 14598, 14786, 14598, 14786 381 581 LYD435 pUC19c_LYD435 Sorghumbicolor 14599, 14787 382 582 LYD436 pUC19c_LYD436 Sorghum bicolor 14600,14788, 14600, 14788 383 758 LYD437 pUC19c_LYD437 SOYBEAN Glycine max14601, 14789, 14921, 15026 384 584 LYD438 pUC19c_LYD438 SOYBEAN Glycinemax 14602, 14790, 14922, 15027 385 585 LYD439 pUC19c_LYD439 SOYBEANGlycine max 14603, 14791, 14923, 15028 386 586 LYD440 pUC19c_LYD440SOYBEAN Glycine max 14604, 14792, 14604, 15029 387 587 LYD441pUC19c_LYD441 SOYBEAN Glycine max 14605, 14793, 14924, 15030 388 588LYD442 pUC19c_LYD442 SOYBEAN Glycine max 14606, 14794, 14606, 14794 389589 LYD443 pMA-RQ_LYD443_GA GeneArt 390 590 LYD445 pUC19d_LYD445 SOYBEANGlycine max 14607, 14795, 14607, 14795 391 591 LYD446 pUC19c_LYD446pSOYBEAN Glycine max 14608, 14796 392 759 LYD448 pUC19c_LYD448 SOYBEANGlycine max 14609, 14797, 14609, 15031 393 594 LYD119 pUC19c_LYD449SOYBEAN Glycine max 14610, 14798, 14610, 15032 394 760 LYD450pUC19c_LYD450 SOYBEAN Glycine max 14611, 14799, 14925, 15033 395 596LYD451 pUC19c_LYD451 SOYBEAN Glycine max 14612, 14800, 14612, 14800 396597 LYD452 pUC19c_LYD452 SOYBEAN Glycine max 14613, 14801, 14613, 14801397 761 LYD453 pUC19c_LYD453 SOYBEAN Glycine max 14614, 14802, 14926,15034 398 599 LYD454 pUC19c_LYD454 SOYBEAN Glycine max 14615, 14803,14615, 14803 399 600 LYD455 pUC19c_LYD455 SOYBEAN Glycine max 14616,14804, 14616, 15035 400 762 LYD456 TopoB_LYD456 SOYBEAN Glycine max14617, 14805, 14927, 15036 401 763 LYD458 pUC19c_LYD458 SOYBEAN Glycinemax 14618, 14806, 14928, 14806 402 603 LYD459 pUC19c_LYD459 SOYBEANGlycine max 14619, 14807, 14619, 14807 403 604 LYD460 pUC19c_LYD460SOYBEAN Glycine max 14620, 14808, 14620, 14808 404 605 LYD461pUC19c_LYD461 SOYBEAN Glycine max 14621, 14809, 14929, 15037 405 606LYD462 pUC19c_LYD462 SOYBEAN Glycine max 14622, 14810, 14622, 15038 406764 LYD465 pUC19c_LYD465 SOYBEAN Glycine max 14623, 14811, 14623, 14811407 608 LYD466 pUC19c_LYD466 SOYBEAN Glycine max 14624, 14812, 14930,15039 408 609 LYD467 pMA-RQ_LYD467_GA GeneArt 409 610 LYD468pMA_LYD468_GA GeneArt 410 611 LYD469 pUC19c_LYD469 SOYBEAN Glycine max14625, 14813, 14625, 14813 411 612 LYD470 pUC19c_LYD470 SOYBEAN Glycinemax 14626, 14814, 14931, 15040 412 765 LYD471 pUC19c_LYD471 SOYBEANGlycine max 14627, 14815, 14627, 15041 413 614 LYD472 pUC19c_LYD472SOYBEAN Glycine max 14628, 14816 414 615 LYD473 pUC19c_LYD473 SOYBEANGlycine max 14629, 14817, 14629, 15043 415 616 LYD474 pUC19c_LYD474SUNFLOWER Helianthus annuus 14630, 14818, 14932, 15044 416 617 LYD475pUC19c_LYD475 TOMATO Lycopersicum ND 14631, 14819, 14933, 15045 417 618LYD477 pUC19_LYD477 TOMATO Lycopersicum ND 14632, 14820, 14934, 15046418 619 LYD478 pUC19c_LYD478 TOMATO Lycopersicum ND 14633, 14821, 14935,15047 419 620 LYD479 pUC19c_LYD479 TOMATO Lycopersicum ND 14634, 14822,14936, 14822 420 621 LYD480 pUC19_LYD480 TOMATO Lycopersicum ND 14635,14823, 14937, 15048 421 766 LYD481 pUC19c_LYD481 TOMATO Lycopersicum ND14636, 14824 422 623 LYD482 pUC19c_LYD482 TOMATO Lycopersicum ND 14637,14825, 14938, 15049 423 624 LYD483 pUC19c_LYD483 TOMATO Lycopersicum ND14638, 14826, 14638, 14826 424 767 LYD484 pUC19c_LYD484 TOMATOLycopersicum ND 14639, 14827, 14939, 15050 425 626 LYD487 pUC19c_LYD487TOMATO Lycopersicum ND 14640, 14828, 14940, 15051 426 768 LYD489pUC19c_LYD489 TOMATO Lycopersicum ND 14641, 14829, 14941, 15052 427 628LYD491 pUC19c_LYD491 TOMATO Lycopersicum ND 14642, 14830, 14942, 14830428 629 LYD492 pUC19c_LYD492 TOMATO Lycopersicum ND 14643, 14831, 14643,15053 429 630 LYD495 pUC19c_LYD495 WHEAT Triticum aestivum L. 14644,14832, 14943, 15054 430 631 LYD496 pUC19c_LYD496 Arabidopsis thalia14669, 14857, 14669, 14857 455 — LYD497 pUC19c_LYD497 Brassica juncea14645, 14833, 14944, 15055 431 769 LYD498 pUC19c_LYD498 Brassica juncea14646, 14834, 14646, 14834 432 633 LYD499 pUC19c_LYD499 Brassica juncea14647, 14835, 14647, 14835 433 634 LYD500 pUC19_LYD500 Brassica juncea14648, 14836, 14648, 14836 434 635 LYD501 pUC19c_LYD501 Brassica juncea14649, 14837, 14945, 15056 435 770 LYD502 pUC19c_LYD502 COTTON Gossypiumbarbadense 14650, 14838 436 771 LYD503 pUC19c_LYD503 MAIZE Zea mays L.14651, 14839, 14946, 15057 437 638 LYD504 pUC19c_LYD504 MEDICAGOMedicago trancatula 14652, 14840, 14652, 15058 438 639 LYD505pUC19c_LYD505 MEDICAGO Medicago trancatula 14653, 14841, 14653, 15059439 772 LYD506 pUC19c_LYD506 MEDICAGO Medicago trancatula 14654, 14842,14947, 15060 440 641 LYD507 pUC19c_LYD507 Sorghum bicolor 14655, 14843,14948, 15061 441 642 LYD508 pUC19d_LYD508 Sorghum bicolor 14656, 14844,14949, 15062 442 643 LYD509 pUC19c_LYD509 Sorghum bicolor 14657, 14845,14657, 14845 443 644 LYD510 pUC19c_LYD510 Sorghum bicolor 14658, 14846,14658, 15063 444 645 LYD511 pUC19c_LYD511 SOYBEAN Glycine max 14659,14847, 14950, 15064 445 646 LYD512 pUC19c_LYD512 SOYBEAN Glycine max14660, 14848 446 647 LYD513 pUC19c_LYD513 SOYBEAN Glycine max 14661,14849 447 648 LYD514 TopoB_LYD514 SOYBEAN Glycine max 14662, 14850,14951, 15065 448 649 LYD515 pUC19c_LYD515 SOYBEAN Glycine max 14663,14851, 14952, 15066 449 650 LYD516 pUC19c_LYD516 SOYBEAN Glycine max14664, 14852, 14953, 15067 450 651 LYD517 pUC19c_LYD517 SOYBEAN Glycinemax 14665, 14853 451 652 LYD518 pUC19c_LYD518 SOYBEAN Glycine max 14666,14854, 14666, 14854 452 773 LYD519 pUC19c_LYD519 SOYBEAN Glycine max14667, 14855, 14954, 15068 453 654 LYD520 pUC19c_LYD520 SOYBEAN Glycinemax 14668, 14856 454 774 “Polyn.”-Polynucleotide; “Polyp.”-polypeptide.For cloning of each gene at least 2 primers were used: Forward (Fwd) orReverse (Rev). In some cases, 4 primers were used: External forward(EF), External reverse (ER), nested forward (NF) or nested reverse (NR).The sequences of the primers used for cloning the genes are provided inthe sequence listing.

Example 15 Production of Transgenic Arabidopsis Plants Expressing theIdentified Polynucleotides of Some Embodiments of the Invention

Experimental Methods

Production of Agrobacterium tumefaciens cells harboring the binaryvectors according to some embodiments of the invention—Each of thebinary vectors described in Example 14 above were used to transformAgrobacterium cells. Two additional binary constructs, having only theAt6669 or the 35S promoter or no additional promoter were used asnegative controls.

The binary vectors were introduced to Agrobacterium tumefaciens GV301,or LB4404 competent cells (about 10⁹ cells/mL) by electroporation. Theelectroporation was performed using a MicroPulser electroporator(Biorad), 0.2 cm cuvettes (Biorad) and EC-2 electroporation program(Biorad). The treated cells were cultured in LB liquid medium at 28° C.for 3 hours, then plated over LB agar supplemented with gentamycin (50mg/L; for Agrobacterium strains GV301) or streptomycin (300 mg/L; forAgrobacterium strain LB4404) and kanamycin (50 mg/L) at 28° C. for 48hours. Abrobacterium colonies, which are developed on the selectivemedia, were further analyzed by PCR using the primers designed to spanthe inserted sequence in the pPI plasmid. The resulting PCR productswere isolated and sequenced to verify that the correct polynucleotidesequences of the invention were properly introduced to the Agrobacteriumcells.

Preparation of Arabidopsis plants for transformation—Arabidopsisthaliana var Columbia (T₀ plants) were transformed according to theFloral Dip procedure [Clough S J, Bent A F. (1998) Floral dip: asimplified method for Agrobacterium-mediated transformation ofArabidopsis thaliana. Plant J. 16(6): 735-43; and Desfeux C, Clough S J,Bent A F. (2000) Female reproductive tissues are the primary targets ofAgrobacterium-mediated transformation by the Arabidopsis floral-dipmethod. Plant Physiol. 123(3): 895-904] with minor modifications.Briefly, Arabidopsis thaliana Columbia (Col0) T₀ plants were sown in 250ml pots filled with wet peat-based growth mix. The pots were coveredwith aluminum foil and a plastic dome, kept at 4° C. for 3-4 days, thenuncovered and incubated in a growth chamber at 18-24° C. under 16/8hours light/dark cycles. The T₀ plants were ready for transformation sixdays before anthesis.

Preparation of the Agrobacterium carrying the binary vectors totransformation into Arabidopsis plants—Single colonies of Agrobacteriumcarrying the binary vectors harboring the genes of some embodiments ofthe invention were cultured in LB medium supplemented with kanamycin (50mg/L) and gentamycin (50 mg/L). The cultures were incubated at 28° C.for 48 hours under vigorous shaking and centrifuged at 4000 rpm for 5minutes. The pellets comprising Agrobacterium cells were resuspended ina transformation medium which contains half-strength (2.15 g/L)Murashige-Skoog (Duchefa); 0.044 μM benzylamino purine (Sigma); 112 μg/LB5 Gambourg vitamins (Sigma); 5% sucrose; and 0.2 ml/L Silwet L-77 (OSISpecialists, CT) in double-distilled water, at pH of 5.7.

Transformation of Arabidopsis plants with theAgrobacterium—Transformation of T₀ plants was performed by invertingeach plant into an Agrobacterium suspension such that the above groundplant tissue is submerged for 3-5 seconds. Each inoculated T₀ plant wasimmediately placed in a plastic tray, then covered with clear plasticdome to maintain humidity and was kept in the dark at room temperaturefor 18 hours to facilitate infection and transformation. Transformed(transgenic) plants were then uncovered and transferred to a greenhousefor recovery and maturation. The transgenic T₀ plants were grown in thegreenhouse for 3-5 weeks until siliques are brown and dry, then seedswere harvested from plants and kept at room temperature until sowing.

Generation of T1 and T2 transgenic plants—For generating T₁ and T₂transgenic plants harboring the genes, seeds collected from transgenicT₀ plants were surface-sterilized by soaking in 70% ethanol for 1minute, followed by soaking in 5% sodium hypochlorite and 0.05% tritonfor 5 minutes. The surface-sterilized seeds were thoroughly washed insterile distilled water then placed on culture plates containinghalf-strength Murashig-Skoog (Duchefa); 2% sucrose; 0.8% plant agar; 50mM kanamycin; and 200 mM carbenicylin (Duchefa). The culture plates wereincubated at 4° C. for 48 hours then transferred to a growth room at 25°C. for an additional week of incubation. Vital T₁ Arabidopsis plantswere transferred to a fresh culture plates for another week ofincubation. Following incubation the T₁ plants were removed from cultureplates and planted in growth mix contained in 250 ml pots. Thetransgenic plants were allowed to grow in a greenhouse to maturity.Seeds harvested from T₁ plants were cultured and grown to maturity as T₂plants under the same conditions as used for culturing and growing theT₁ plants.

Example 16 Evaluation of Transgenic Arabidopsis for Seed Yield and PlantGrowth Rate Under Normal Conditions in Greenhouse Assays (GH-SM Assays)

Assay 1: Seed yield plant biomass and plant growth rate under normalgreenhouse conditions—This assay follows seed yield production, thebiomass formation and the rosette area growth of plants grown in thegreenhouse at non-limiting nitrogen growth conditions. TransgenicArabidopsis seeds were sown in agar media supplemented with % MS mediumand a selection agent (Kanamycin). The T2 transgenic seedlings were thentransplanted to 1.7 trays filled with peat and perlite in a 1:1 ratio.The trays were irrigated with a solution containing 6 mM inorganicnitrogen in the form of KNO₃ with 1 mM KH₂PO₄, 1 mM MgSO₄. 2 mM CaCl₂and microelements. All plants were grown in the greenhouse until matureseeds. Seeds were harvested, extracted and weight. The remaining plantbiomass (the above ground tissue) was also harvested, and weightedimmediately or following drying in oven at 50° C. for 24 hours.

Each construct was validated at its T2 generation. Transgenic plantstransformed with a construct conformed by an empty vector carrying theAt6669 promoter and the selectable marker was used as control.

The plants were analyzed for their overall size, growth rate, flowering,seed yield, 1,000-seed weight, dry matter and harvest index (HI-seedyield/dry matter). Transgenic plants performance was compared to controlplants grown in parallel under the same conditions. Mock-transgenicplants expressing the uidA reporter gene (GUS-Intron) or with no gene atall, under the same promoter were used as control.

The experiment was planned in nested randomized plot distribution. Foreach gene of the invention three to five independent transformationevents were analyzed from each construct.

Digital imaging—A laboratory image acquisition system, which consists ofa digital reflex camera (Canon EOS 300D) attached with a 55 mm focallength lens (Canon EF-S series), mounted on a reproduction device(Kaiser RS), which includes 4 light units (4×150 Watts light bulb) wasused for capturing images of plant samples.

The image capturing process was repeated every 2 days starting from day1 after transplanting till day 15. Same camera, placed in a custom madeiron mount, was used for capturing images of larger plants sawn in whitetubs in an environmental controlled greenhouse. The tubs are squareshape include 1.7 liter trays. During the capture process, the tubs wereplaced beneath the iron mount, while avoiding direct sun light andcasting of shadows.

An image analysis system was used, which consists of a personal desktopcomputer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ1.39 [Java based image processing program which was developed at theU.S. National Institutes of Health and freely available on the internetat Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Imageswere captured in resolution of 10 Mega Pixels (3888×2592 pixels) andstored in a low compression JPEG (Joint Photographic Experts Groupstandard) format. Next, analyzed data was saved to text files andprocessed using the JMP statistical analysis software (SAS institute).

Leaf analysis—Using the digital analysis leaves data was calculated,including leaf number, rosette area, rosette diameter, and leaf bladearea.

Vegetative growth rate: the relative growth rate (RGR) of leaf number[formula IX (described above)], rosette area [formula VI (describedabove)], plot coverage (formula XIII, below) and harvest index [formulaIV (described above)] was calculated with the indicated formulas.

Relative growth rate of plot coverage=Regression coefficient of plotcoverage along time course.  Formula XII

Seeds average weight—At the end of the experiment all seeds werecollected. The seeds were scattered on a glass tray and a picture wastaken. Using the digital analysis, the number of seeds in each samplewas calculated.

Dry weight and seed yield—On about day 80 from sowing, the plants wereharvested and left to dry at 30° C. in a drying chamber. The biomass andseed weight of each plot were measured and divided by the number ofplants in each plot. Dry weight=total weight of the vegetative portionabove ground (excluding roots) after drying at 30° C. in a dryingchamber, Seed yield per plant=total seed weight per plant (gr). 1000seed weight (the weight of 1000 seeds) (gr.).

The harvest index (HI) was calculated using Formula IV as describedabove.

Oil percentage in seeds—At the end of the experiment all seeds from eachplot were collected. Seeds from 3 plots were mixed grounded and thenmounted onto the extraction chamber. 210 ml of n-Hexane (Cat No. 080951Biolab Ltd.) were used as the solvent. The extraction was performed for30 hours at medium heat 50° C. Once the extraction has ended then-Hexane was evaporated using the evaporator at 35° C. and vacuumconditions. The process was repeated twice. The information gained fromthe Soxhlet extractor (Soxhlet, F. Die gewichtsanalytische Bestimmungdes Milchfettes, Polytechnisches J. (Dingler's) 1879, 232, 461) was usedto create a calibration curve for the Low Resonance NMR. The content ofoil of all seed samples was determined using the Low Resonance NMR(MARAN Ultra-Oxford Instrument) and its MultiQuant software package.

Silique length analysis—On day 50 from sowing, 30 siliques fromdifferent plants in each plot were sampled in block A. The chosensiliques were green-yellow in color and were collected from the bottomparts of a grown plant's stem. A digital photograph was taken todetermine silique's length.

Statistical analyses—To identify outperforming genes and constructs,results from the independent transformation events tested were analyzedseparately. Data was analyzed using Student's t-test and results areconsidered significant if the p value was less than 0.1. The JMPstatistics software package was used (Version 5.2.1, SAS Institute Inc.,Cary, N.C., USA).

Tables 56-60 summarize the observed phenotypes of transgenic plantsexogenously expressing the gene constructs using the seed maturation(GH-SM) assays under normal conditions. The evaluation of each gene wasperformed by testing the performance of different number of events.Event with p-value <0.1 was considered statistically significant.

TABLE 56 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Gene Dry Weight [mg]Flowering Inflorescence Emergence Name Event # Ave. P-Val. % Incr. Ave.P-Val. % Incr. Ave. P-Val. % Incr. LYD513 67217.3 — — — 38.5 0.02 −332.1 0.28 −1 LYD512 67209.1 — — — 38.6 0.13 −2 32.0 0.15 −1 LYD51267209.4 — — — — — — 32.1 0.28 −1 LYD512 67211.1 — — — — — — 32.1 0.28 −1LYD512 67212.2 — — — — — — 32.1 0.28 −1 LYD482 67334.1 — — — — — — 32.10.28 −1 LYD482 67334.3 — — — — — — 32.0 0.15 −1 LYD475 67202.3 — — —38.8 0.07 −2 — — — LYD475 67204.4 — — — 38.0 0.02 −4 32.0 0.15 −1 LYD47267332.1 — — — 37.6 L −5 32.0 0.15 −1 LYD472 67332.3 — — — 38.7 0.04 −232.0 0.15 −1 LYD472 67332.4 — — — 38.0 0.02 −4 32.0 0.15 −1 LYD46667119.4 — — — — — — 32.1 0.28 −1 LYD466 67121.1 — — — 37.5 L −5 32.00.15 −1 LYD466 67121.3 — — — — — — 32.1 0.28 −1 LYD452 67106.2 — — — — —— 32.0 0.15 −1 LYD451 67187.7 — — — — — — 32.1 0.28 −1 LYD451 67188.1 —— — 38.9 0.11 −1 32.1 0.28 −1 LYD451 67188.4 — — — 38.3 0.26 −3 — — —LYD445 67353.1 — — — — — — 32.0 0.15 −1 LYD445 67353.2 — — — 38.5 0.02−3 32.0 0.15 −1 LYD439 67095.6 — — — 39.0 0.20 −1 32.1 0.28 −1 LYD41567264.5 — — — 38.8 0.07 −2 — — — LYD415 67266.1 — — — 39.0 0.20 −1 32.10.28 −1 LYD382 67175.2 — — — — — — 32.1 0.28 −1 LYD382 67176.3 — — — — —— 32.0 0.15 −1 LYD339 67246.3 — — — — — — 32.0 0.15 −1 LYD339 67247.6 —— — — — — 32.0 0.15 −1 LYD324 67167.1 — — — 38.7 0.08 −2 32.0 0.15 −1LYD321 67280.1 — — — — — — 32.1 0.28 −1 LYD321 67283.1 — — — — — — 32.10.28 −1 LYD321 67283.4 — — — 38.0 0.02 −4 32.0 0.15 −1 LYD302 67413.1 —— — — — — 32.1 0.28 −1 LYD302 67414.2 — — — — — — 32.1 0.28 −1 LYD30267416.3 — — — 38.7 0.04 −2 32.0 0.15 −1 LYD296 67358.6 — — — 38.8 0.08−2 32.1 0.28 −1 LYD296 67360.1 — — — 38.7 0.09 −2 — — — LYD290 67233.1 —— — 39.0 0.20 −1 32.1 0.28 −1 LYD290 67233.5 — — — 38.6 0.03 −2 — — —CONT. — — — — 39.5 — — 32.3 — — LYD517 67222.1 — — — 37.5 0.05 −3 32.00.23 −1 LYD515 67151.1 — — — 37.1 0.18 −4 32.0 0.23 −1 LYD502 67341.5 —— — 37.5 0.05 −3 32.0 0.23 −1 LYD502 67342.2 — — — — — — 32.0 0.23 −1LYD498 67252.3 — — — — — — 32.0 0.23 −1 LYD492 67364.1 — — — — — — 32.00.23 −1 LYD492 67366.3 — — — 37.1 0.06 −4 — — — LYD474 67199.1 — — —37.7 0.10 −2 32.0 0.23 −1 LYD454 67192.5 — — — 37.6 0.07 −3 — — — LYD45067178.4 — — — 37.6 0.07 −3 — — — LYD450 67182.2 — — — 37.6 0.07 −3 32.00.23 −1 LYD397 67322.1 — — — 37.6 0.07 −3 32.0 0.23 −1 LYD397 67324.2 —— — 37.1 0.06 −4 32.0 0.23 −1 LYD328 67238.2 — — — 37.1 0.06 −4 32.00.23 −1 LYD323 67286.4 — — — — — — 32.0 0.23 −1 LYD323 67287.1 — — —37.0 0.12 −4 32.0 0.23 −1 LYD323 67287.3 — — — 36.8 0.01 −5 32.0 0.23 −1LYD312 67256.4 — — — 37.5 0.05 −3 32.0 0.23 −1 LYD312 67256.5 — — — 37.60.07 −3 32.0 0.23 −1 LYD312 67257.1 — — — 37.9 0.29 −2 32.0 0.23 −1LYD312 67257.3 — — — 37.5 0.05 −3 32.0 0.23 −1 LYD310 67160.2 — — — 38.00.29 −1 32.0 0.23 −1 LYD301 67347.1 — — — 37.9 0.29 −2 32.0 0.23 −1LYD301 67347.2 — — — 37.1 0.06 −4 32.0 0.23 −1 LYD298 66962.3 — — — 37.90.29 −2 32.0 0.23 −1 LYD298 66964.4 — — — 37.5 0.05 −3 32.0 0.23 −1LYD298 66966.1 — — — 37.6 0.07 −3 — — — LYD291 67402.2 — — — — — — 32.00.23 −1 CONT. — — — — 38.6 — — 32.4 — — LYD508 67823.2 1170.6 0.04 9 — —— — — — LYD508 67824.3 1310.0 0.22 22 37.9 0.08 −4 31.8 0.13 −2 LYD49567731.2 1120.0 0.26 5 — — — — — — LYD495 67732.5 1178.1 0.23 10 — — — —— — LYD491 67874.3 1120.0 0.26 5 — — — — — — LYD491 67874.6 1187.5 0.0311 — — — — — — LYD489 67784.4 1118.8 0.29 4 — — — — — — LYD479 67727.41198.8 0.02 12 — — — — — — LYD433 67702.4 1228.8 L 15 — — — — — — LYD42867472.2 — — — 38.5 0.22 −3 32.0 0.20 −1 LYD428 67473.3 1204.4 0.17 1237.6 0.14 −5 31.6 0.22 −3 LYD305 67533.1 1353.1 L 26 — — — — — — CONT. —1071.0 — — 39.6 — — 32.5 — — LYD484 67133.3 — — — — — — 27.8 0.03 −4LYD484 67135.3 — — — 34.8 0.08 −2 27.8 0.02 −4 LYD470 67125.4 — — — 34.50.02 −3 27.9 0.02 −4 LYD470 67126.7 — — — 33.8 0.28 −5 27.0 0.27 −7LYD459 67112.1 — — — — — — 27.4 0.24 −6 LYD414 67091.1 — — — 33.8 0.28−5 — — — LYD414 67091.2 — — — 33.7 0.16 −5 28.3 0.19 −2 LYD387 67316.1 —— — 34.7 0.17 −2 — — — LYD387 67317.1 — — — — — — 28.0 0.03 −3 LYD38767317.4 — — — — — — 27.9 0.03 −4 LYD386 67860.3 — — — — — — 28.1 0.04 −3LYD347 67848.2 — — — 34.5 0.02 −3 27.2 0.13 −6 LYD341 67055.2 — — — 34.80.08 −2 27.3 0.20 −6 LYD338 67442.3 — — — 33.9 0.26 −4 28.0 0.03 −3LYD338 67443.1 — — — 34.7 0.17 −2 — — — LYD337 66994.3 — — — 34.3 L −3 —— — LYD337 66995.4 — — — 33.8 0.28 −5 27.3 0.20 −6 LYD322 66884.2 — — —33.8 0.28 −5 27.5 0.13 −5 LYD322 66886.6 — — — 34.5 0.02 −3 — — — LYD32266887.1 — — — 33.1 L −7 — — — LYD307 66977.3 — — — — — — 27.4 0.24 −6CONT. — — — — 35.5 — — 29.0 — — LYD496 67737.2 — — — — — — 31.5 0.18 −2LYD496 67739.1 — — — 37.1 0.11 −3 — — — LYD496 67741.6 — — — — — — 31.20.06 −2 LYD410 67546.3 1274.9 0.18 12 — — — 31.1 0.04 −3 LYD409 67468.21203.1 0.05 6 — — — — — — LYD405 67696.2 — — — — — — 31.6 0.28 −1 LYD40367769.4 1375.0 L 21 — — — — — — LYD403 67771.1 — — — — — — 31.4 0.18 −2LYD402 67760.2 1203.1 0.14 6 37.1 0.29 −3 — — — LYD379 67677.1 1181.90.14 4 — — — — — — LYD379 67678.1 — — — — — — 31.5 0.18 −2 LYD37267673.4 1281.2 0.23 13 37.1 0.11 −3 31.2 0.06 −2 LYD366 67812.5 1192.50.08 5 — — — — — — LYD362 67538.2 1175.0 0.20 3 — — — — — — LYD36267543.5 — — — 36.7 0.02 −4 31.3 0.21 −2 LYD355 67641.2 1180.0 0.15 4 — —— — — — LYD347 67844.2 1213.8 0.03 7 — — — 31.3 0.21 −2 LYD335 67557.5 —— — — — — 31.5 0.18 −2 CONT. — 1135.6 — — 38.1 — — 32.0 — — LYD50467136.3 — — — 33.0 L −8 26.8 L −8 LYD504 67138.1 — — — 34.7 0.04 −3 27.90.02 −5 LYD504 67139.1 — — — — — — 27.6 0.16 −6 LYD504 67140.1 — — —34.6 0.08 −3 — — — LYD466 67119.4 — — — 34.0 L −5 28.1 L −4 LYD44267103.1 — — — — — — 28.0 L −4 LYD442 67104.3 — — — 34.7 0.06 −3 28.10.01 −4 LYD440 66902.1 — — — — — — 28.4 0.28 −3 LYD440 66903.1 — — —34.7 0.06 −3 27.8 L −5 LYD425 67454.5 — — — 35.1 0.17 −2 28.1 L −4LYD408 67304.1 — — — 34.4 0.02 −4 — — — LYD408 67305.6 — — — 34.7 0.11−3 27.9 L −5 LYD408 67306.2 — — — 34.1 0.01 −5 28.0 L −4 LYD401 67086.3— — — 34.9 0.09 −2 — — — LYD375 67071.4 — — — 34.9 0.18 −2 — — — LYD37567073.2 — — — 34.4 0.02 −4 28.0 L −4 LYD342 67062.1 — — — 34.9 0.09 −228.4 0.28 −3 LYD329 67277.4 — — — 34.4 0.16 −4 28.0 L −4 LYD320 67040.3— — — 34.8 0.09 −3 28.4 0.28 −3 LYD318 66980.5 — — — 35.0 0.16 −2 — — —LYD318 66982.1 — — — 34.9 0.19 −2 — — — LYD318 66983.4 — — — 33.4 0.03−6 27.3 0.18 −7 LYD316 67436.1 — — — 34.7 0.06 −3 — — — LYD316 67439.1 —— — 34.7 0.06 −3 — — — LYD298 66962.3 — — — 35.1 0.17 −2 — — — LYD29266998.3 — — — 34.5 0.03 −3 27.5 L −6 LYD292 66999.4 — — — 34.4 0.16 −428.4 0.25 −3 LYD292 67000.1 — — — 34.4 0.02 −4 28.9 0.28 −1 CONT. — — —— 35.8 — — 29.2 — — Table 56. “CONT.”—Control; “Ave.”—Average; “% Incr.”= % increment; “p-val.”—p-value, L—p < 0.01. The transgenes were underthe transcriptional regulation of the new At6669 promoter (SEQ ID NO:14467). “—“ = results are still unavailable.

TABLE 57 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Gene Leaf Blade Area[cm²] Leaf Number Plot Coverage [cm²] Name Event # Ave. P-Val. % Incr.Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD499 68152.2 1.1 0.22 7 — — —— — — LYD446 68110.1 1.1 0.14 15 — — — 63.1 0.03 18 LYD443 68163.1 1.10.05 15 — — — 62.3 0.14 17 LYD443 68164.1 1.0 0.06 4 — — — — — — LYD44368164.2 1.2 L 18 — — — 64.2 0.12 20 LYD443 68165.3 1.1 L 12 9.8 0.25 362.8 L 18 LYD436 68073.3 1.1 0.09 15 10.1 0.05 5 64.4 0.02 21 LYD41667904.3 1.0 0.21 4 — — — 56.4 0.03 6 LYD416 67907.6 1.0 0.19 6 — — — — —— LYD391 68156.4 1.0 0.15 5 — — — 58.0 L 9 LYD391 68160.4 1.2 L 22 — — —68.4 0.09 28 LYD388 68096.2 1.2 L 19 — — — 63.4 L 19 LYD388 68098.2 1.20.04 25 — — — 69.1 L 29 LYD388 68098.3 1.1 L 14 — — — 57.9 0.14 9 LYD36768066.5 1.2 0.01 25 — — — 68.7 0.14 29 LYD364 68018.4 1.1 0.17 12 — — —60.2 0.03 13 LYD364 68020.1 1.1 0.07 8 — — — 55.3 0.29 3 LYD364 68020.51.3 0.05 26 9.9 0.22 3 72.5 L 36 LYD364 68022.1 1.1 0.14 14 — — — 62.50.15 17 LYD361 68147.1 1.0 0.12 4 — — — 56.2 0.25 5 LYD360 68061.1 1.20.11 19 — — — 65.1 0.02 22 LYD360 68063.2 1.1 0.04 12 — — — 58.2 0.26 9LYD357 68228.1 1.1 L 9 — — — 57.8 0.20 8 LYD354 68133.4 1.1 0.12 12 — —— 61.7 0.11 16 LYD354 68133.6 1.1 0.14 8 — — — — — — LYD349 68085.5 1.40.11 38 9.8 0.25 3 76.9 0.08 44 LYD308 66881.2 1.1 0.25 14 9.9 0.22 363.2 0.02 18 LYD295 67972.2 — — — 10.0 0.07 5 63.3 0.17 18 LYD29567972.4 — — — — — — 61.8 0.20 16 CONT. — 1.0 — — 9.6 — — 53.4 — — LYD51367217.3 0.9 L 19 — — — 49.3 L 22 LYD512 67209.1 0.8 0.27 11 — — — — — —LYD482 67334.1 0.8 0.26 11 — — — — — — LYD482 67336.1 0.8 0.19 8 — — — —— — LYD475 67204.4 0.8 L 13 — — — 47.9 L 18 LYD472 67332.1 0.9 0.09 19 —— — 49.7 0.06 23 LYD472 67332.4 0.9 L 23 — — — 49.9 L 23 LYD466 67121.10.9 L 17 — — — 49.0 L 21 LYD452 67106.2 0.8 0.20 5 — — — 43.4 0.20 7LYD451 67187.9 0.8 0.10 6 — — — 43.8 0.09 8 LYD451 67188.1 0.8 0.30 10 —— — — — — LYD451 67188.4 0.8 0.14 13 — — — 47.5 0.07 17 LYD445 67352.3 —— — 9.8 0.27 2 — — — LYD445 67353.1 0.8 0.20 7 — — — 43.5 0.27 7 LYD44567353.2 0.8 L 12 — — — 46.8 L 16 LYD445 67354.5 — — — — — — 42.7 0.29 6LYD439 67094.1 0.8 0.17 12 — — — — — — LYD439 67094.3 0.8 0.29 10 — — —47.2 0.06 17 LYD439 67095.6 0.8 L 12 — — — 45.9 0.02 13 LYD415 67262.10.8 0.07 9 — — — 44.7 0.21 11 LYD415 67264.5 — — — — — — 43.5 0.13 7LYD415 67266.6 0.8 0.28 7 — — — — — — LYD382 67174.1 0.8 0.30 15 — — —45.8 0.19 13 LYD382 67175.2 0.9 0.10 16 — — — 47.4 0.16 17 LYD33967247.3 0.8 0.11 6 — — — — — — LYD324 67167.1 — — — 9.8 0.17 2 — — —LYD321 67280.1 — — — 9.9 0.07 3 — — — LYD321 67283.1 0.8 L 14 — — — 47.80.01 18 LYD321 67283.3 0.8 0.16 9 — — — — — — LYD321 67283.4 1.0 0.10 34— — — 55.2 0.04 36 LYD302 67414.3 0.9 L 16 — — — 46.2 0.03 14 LYD30267416.3 0.8 0.03 13 — — — 45.5 0.02 12 LYD296 67358.6 0.9 0.24 21 — — —50.1 0.14 24 LYD296 67360.4 — — — 9.8 0.17 2 — — — LYD290 67233.3 0.80.26 4 — — — — — — CONT. — 0.7 — — 9.6 — — 40.5 — — LYD517 67221.3 — — —— — — 30.1 0.14 6 LYD517 67222.1 0.6 0.22 14 — — — — — — LYD515 67151.10.6 0.01 18 — — — 33.3 0.08 17 LYD515 67152.4 0.7 L 26 — — — 36.7 L 29LYD502 67340.4 0.6 0.19 9 — — — 31.9 0.09 13 LYD502 67341.5 0.6 0.04 159.6 0.07 5 32.6 0.04 15 LYD502 67342.1 — — — 9.4 0.16 2 — — — LYD50267342.6 0.6 0.14 9 — — — 31.5 0.02 11 LYD498 67252.3 0.6 0.04 15 9.40.16 2 33.3 L 17 LYD498 67254.1 0.6 0.06 14 — — — 31.2 0.06 10 LYD49867254.3 0.6 0.03 15 — — — 32.9 0.01 16 LYD492 67364.5 0.6 0.24 13 — — —31.6 0.20 11 LYD474 67196.1 0.6 0.26 12 — — — — — — LYD474 67199.1 0.60.23 10 9.5 0.15 4 30.8 0.05 9 LYD454 67192.5 0.6 0.04 19 — — — 33.50.02 18 LYD450 67178.3 0.6 0.10 13 9.9 0.16 8 32.5 0.02 14 LYD45067180.2 — — — — — — 31.6 0.27 11 LYD450 67182.2 0.6 0.01 18 9.6 0.03 433.5 0.01 18 LYD428 67474.4 — — — 9.6 0.22 4 — — — LYD397 67322.1 — — —— — — 30.1 0.28 6 LYD397 67324.2 0.7 L 29 — — — 36.3 0.04 28 LYD32367286.1 0.6 0.19 13 — — — 33.0 0.29 16 LYD323 67287.3 0.6 0.04 15 — — —32.8 L 16 LYD312 67256.4 0.7 0.06 28 9.8 0.04 6 37.0 0.08 30 LYD31267256.5 0.6 0.03 15 — — — 32.9 L 16 LYD310 67161.1 0.6 0.22 8 — — — 31.70.04 12 LYD310 67164.1 — — — — — — 30.5 0.08 7 LYD301 67347.2 0.7 0.0528 — — — 35.5 0.01 25 LYD301 67347.4 0.6 0.10 12 9.6 0.03 4 31.7 0.13 12LYD298 66964.4 0.6 0.02 21 9.4 0.16 2 35.3 0.15 24 LYD298 66966.2 0.60.06 12 — — — 32.7 L 15 LYD291 67400.2 — — — 9.6 0.22 4 — — — LYD29167402.2 0.6 0.14 11 — — — — — — CONT. — 0.5 — — 9.2 — — 28.4 — — LYD50867823.1 — — — 9.9 0.26 4 — — — LYD508 67823.2 0.8 0.15 8 — — — 44.8 0.137 LYD508 67824.3 0.9 L 16 10.2 0.10 6 49.5 0.08 18 LYD503 67527.1 — — —10.2 0.01 6 — — — LYD501 67887.3 — — — 10.1 0.21 6 — — — LYD497 67880.3— — — 10.2 0.10 6 — — — LYD497 67881.4 — — — 9.8 0.23 2 — — — LYD49767883.2 — — — 10.0 0.05 4 — — — LYD497 67883.4 0.8 0.03 9 — — — 46.00.03 10 LYD479 67727.4 0.9 0.08 20 10.1 0.05 6 53.6 0.21 28 LYD44867917.2 — — — 9.9 0.22 3 — — — LYD441 67715.4 — — — 9.9 0.22 3 — — —LYD428 67473.3 0.9 L 21 10.3 0.21 8 54.1 L 29 LYD428 67474.4 0.8 0.08 8— — — — — — CONT. — 0.7 — — 9.6 — — 42.0 — — LYD484 67135.2 1.0 0.08 7 —— — — — — LYD484 67135.3 1.0 0.21 5 — — — 64.6 0.05 6 LYD470 67126.7 1.10.06 17 — — — 72.5 L 20 LYD470 67127.3 — — — — — — 61.9 0.25 2 LYD45967116.4 1.0 0.22 5 — — — — — — LYD414 67089.4 1.0 L 7 — — — — — — LYD41467091.1 1.0 0.25 4 — — — — — — LYD387 67317.4 1.1 L 16 11.8 0.17 7 75.40.06 24 LYD347 67845.1 1.0 0.27 3 — — — — — — LYD347 67848.2 1.0 0.04 7— — — — — — LYD341 67054.2 1.0 0.16 3 — — — — — — LYD338 67442.3 1.1 L15 11.5 0.25 4 73.2 0.12 21 LYD337 66994.3 1.0 0.29 4 — — — 62.8 0.12 4LYD337 66995.5 — — — — — — 65.5 0.23 8 LYD322 66884.2 1.0 L 13 — — —68.6 L 13 LYD322 66887.1 — — — — — — 66.0 0.02 9 LYD307 66975.3 — — — —— — 65.0 0.05 7 LYD307 66975.4 1.0 0.02 6 — — — — — — LYD307 66976.3 1.0L 7 — — — — — — LYD307 66977.3 1.0 0.07 13 — — — 69.9 0.13 15 LYD30367300.6 1.0 0.14 4 — — — — — — LYD293 66958.1 1.0 0.09 4 — — — — — —CONT. — 0.9 — — 11.0 — — 60.7 — — LYD410 67546.3 — — — 10.8 0.12 11 — —— LYD409 67467.5 0.8 0.01 8 — — — — — — LYD409 67468.1 0.8 0.21 6 — — —— — — LYD405 67694.4 — — — 10.1 0.10 3 — — — LYD405 67697.2 — — — 9.90.28 2 — — — LYD379 67678.1 0.8 0.02 8 10.1 0.10 3 51.1 0.13 11 LYD37267673.3 — — — 10.1 0.12 4 — — — LYD348 67850.1 — — — 10.0 0.16 3 — — —LYD335 67558.2 — — — 10.1 0.28 3 — — — CONT. — 0.8 — — 9.7 — — 45.9 — —LYD489 67785.4 1.0 L 13 — — — 52.0 0.18 6 LYD489 67787.3 — — — 9.5 L 6 —— — LYD483 68056.5 1.0 0.25 6 — — — — — — LYD472 67330.6 1.0 0.02 8 — —— — — — LYD472 67332.4 1.0 0.03 12 — — — 54.0 0.18 10 LYD456 67964.1 — —— 9.4 0.17 5 — — — LYD456 67966.3 1.0 0.07 6 — — — 53.4 0.06 8 LYD45667967.4 0.9 0.25 4 9.3 0.26 4 51.5 0.14 5 LYD423 68216.3 — — — 9.2 0.193 — — — LYD423 68218.3 — — — 9.4 0.17 5 — — — LYD422 68103.3 1.0 0.16 11— — — — — — LYD422 68103.4 1.0 0.01 9 — — — — — — LYD417 68042.2 — — —9.4 0.17 5 — — — LYD417 68043.1 0.9 0.10 5 — — — — — — LYD417 68043.51.0 0.23 6 — — — — — — LYD392 68032.2 1.0 0.12 15 — — — 53.4 0.21 8LYD392 68033.3 1.0 0.13 16 9.4 0.09 5 58.1 L 18 LYD392 68035.1 1.0 0.298 — — — — — — LYD376 68025.1 — — — 9.2 0.15 3 — — — LYD376 68025.3 — — —9.1 0.24 2 — — — LYD376 68026.5 — — — 9.2 0.15 3 — — — LYD365 68092.41.0 0.02 8 — — — 52.8 0.13 7 LYD365 68092.5 1.1 0.08 16 9.6 0.12 7 57.90.22 18 LYD365 68093.2 1.0 0.07 15 9.2 0.06 3 53.3 0.17 8 LYD359 67946.31.0 0.01 10 9.2 0.19 3 51.7 0.29 5 LYD359 67947.2 1.0 0.19 8 — — — — — —LYD359 67949.4 — — — 9.7 0.22 8 — — — LYD351 68126.2 1.0 L 14 — — — 55.8L 13 LYD351 68129.3 1.0 0.04 7 — — — — — — LYD351 68129.5 1.0 0.26 10 —— — 52.4 0.14 6 LYD306 66971.1 1.0 L 13 — — — 56.4 L 14 LYD299 68115.4 —— — 9.4 0.09 5 — — — LYD299 68115.7 1.1 L 21 — — — 57.4 L 17 CONT. — 0.9— — 9.0 — — 49.2 — — LYD506 67144.2 1.0 0.02 16 11.4 0.26 6 67.1 0.01 19LYD506 67146.2 1.1 0.19 18 11.8 0.30 8 70.2 0.10 24 LYD504 67136.2 1.00.23 7 11.5 0.30 6 63.0 0.04 12 LYD504 67136.3 1.0 0.04 15 12.2 0.02 1269.6 L 23 LYD504 67138.1 — — — — — — 62.5 0.16 11 LYD504 67139.1 1.00.02 17 11.6 L 7 69.0 0.02 22 LYD504 67140.1 — — — 11.4 0.05 5 61.8 0.139 LYD466 67119.4 1.0 0.13 8 — — — 61.0 0.24 8 LYD442 67104.3 1.0 0.14 1511.4 0.22 5 69.3 0.20 23 LYD440 66902.1 1.0 0.12 12 — — — 66.3 0.08 17LYD440 66902.2 1.0 0.06 12 11.1 0.20 2 65.6 0.08 16 LYD440 66905.1 — — —11.1 0.20 2 — — — LYD440 66906.1 1.0 0.06 12 11.3 0.02 4 67.4 L 19LYD432 67959.2 1.0 0.14 15 11.4 0.26 6 69.2 0.22 22 LYD432 67961.2 1.00.07 11 — — — 67.5 L 19 LYD425 67454.3 — — — 11.6 L 7 62.8 0.05 11LYD425 67454.5 1.0 0.24 11 — — — 64.7 0.15 15 LYD408 67304.1 1.1 0.01 1911.8 L 8 74.3 L 32 LYD408 67305.6 1.1 L 23 — — — 74.5 0.07 32 LYD40867306.2 1.0 0.13 9 11.4 0.10 6 63.4 0.09 12 LYD401 67084.2 1.0 0.11 9 —— — 60.9 0.17 8 LYD375 67070.2 1.0 0.26 9 — — — 64.0 0.05 13 LYD37567073.2 1.1 0.02 19 — — — 65.9 0.03 17 LYD342 67059.4 1.0 0.07 11 — — —64.0 0.03 13 LYD342 67062.1 1.0 0.01 18 12.0 0.16 11 72.6 L 28 LYD32967275.1 — — — — — — 59.6 0.26 6 LYD329 67277.4 — — — — — — 65.4 0.04 16LYD320 67040.2 — — — 11.6 L 7 59.7 0.24 6 LYD320 67043.1 1.0 0.20 7 — —— 60.1 0.20 6 LYD318 66980.3 — — — — — — 60.8 0.14 8 LYD318 66980.5 — —— — — — 62.6 0.08 11 LYD318 66982.1 — — — 11.6 L 7 63.8 0.03 13 LYD31866983.4 1.0 0.03 15 12.3 0.08 14 70.6 L 25 LYD316 67436.1 1.0 0.24 1111.7 0.05 8 64.7 0.02 14 LYD316 67437.2 1.0 0.05 12 — — — 65.1 0.02 15LYD316 67439.1 1.0 0.01 17 11.8 0.10 8 69.6 L 23 LYD298 66963.4 — — —11.8 0.21 8 — — — LYD292 66998.3 1.0 0.01 17 11.6 0.01 7 68.3 L 21LYD292 66999.2 1.1 0.04 24 11.6 0.13 7 74.8 0.05 32 LYD292 66999.4 1.00.16 12 — — — 64.7 0.14 15 LYD292 67000.1 1.1 0.02 21 — — — 75.6 0.01 34CONT. — 0.9 — — 10.8 — — 56.5 — — LYD362 67543.5 0.75 0.12 10.2 — — — —— — LYD362 67541.3 0.75 0.13 10 — — — — — — LYD362 67538.2 0.74 0.15 9.3— — — — — — LYD362 67543.3 0.72 0.32 6.3 — — — — — — LYD362 67543.6 0.720.34 6.1 — — — — — — LYD366 67810.1 0.74 0.18 8.5 — — — — — — LYD36667812.5 0.73 0.29 6.8 — — — — — — LYD386 67860.3 0.71 0.47 4.5 — — — — —— LYD386 67856.1 0.71 0.50 4.2 — — — — — — CONT. — 0.68 — — — — — — — —LYD362 67543.5 0.74 0.06 12.3 — — — — — — LYD362 67541.3 0.74 0.06 12.2— — — — — — LYD362 67538.2 0.74 0.07 12.0 — — — — — — LYD362 67543.30.73 0.11 10.6 — — — — — — LYD362 67543.6 0.73 0.11 10.5 — — — — — —LYD366 67810.1 0.72 0.16 9.2 — — — — — — LYD366 67812.5 0.72 0.19 8.4 —— — — — — LYD366 67808.2 0.71 0.27 7.0 — — — — — — LYD366 67812.1 0.700.33 6.1 — — — — — — LYD366 67810.4 0.70 0.38 5.6 — — — — — — LYD38667860.3 0.70 0.39 5.3 — — — — — — LYD386 67856.1 0.69 0.41 5.2 — — — — —— CONT. — 0.66 — — — — — — — — LYD434 67978.2 — — — 9.7 0.22 3.1 — — —LYD434 67977.3 — — — 9.6 0.32 2.1 — — — CONT. — — — — 9.4 — — — — —Table 57. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment;“p-val.”—p-value, L—p < 0.01. The transgenes were under thetranscriptional regulation of the new At6669 promoter (SEQ ID NO:14467). “—“ = results are still unavailable.

TABLE 58 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Gene RGR Of Leaf NumberRGR Of Plot Coverage RGR Of Rosette Diameter Name Event # Ave. P-Val. %Incr. Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD446 68109.4 — — — 8.20.23 15 0.5 0.16 9 LYD446 68110.1 — — — 8.4 0.13 18 — — — LYD443 68163.1— — — 8.3 0.15 16 0.5 0.14 8 LYD443 68164.2 — — — 8.7 0.07 21 0.5 0.13 8LYD443 68165.3 — — — 8.4 0.11 18 0.5 0.05 11 LYD436 68073.1 — — — — — —0.5 0.26 7 LYD436 68073.3 — — — 8.7 0.07 22 0.5 0.20 7 LYD436 68075.3 —— — 8.9 0.07 24 0.5 0.09 12 LYD416 67904.3 0.7 0.29 16 — — — — — —LYD416 67907.6 — — — — — — 0.5 0.22 7 LYD391 68160.4 — — — 9.2 0.02 290.5 0.01 15 LYD388 68096.2 — — — 8.5 0.09 19 0.5 0.09 9 LYD388 68098.2 —— — 9.3 0.01 30 0.5 0.02 12 LYD388 68098.3 — — — — — — 0.5 0.18 7 LYD38868098.4 — — — 8.7 0.08 22 0.5 0.14 9 LYD367 68066.1 — — — 8.1 0.28 140.5 0.19 9 LYD367 68066.5 — — — 9.2 0.02 29 0.5 0.02 13 LYD367 68066.6 —— — 8.5 0.15 19 0.5 0.20 8 LYD367 68068.5 — — — 8.4 0.16 17 0.5 0.15 8LYD364 68018.3 — — — 8.2 0.23 15 0.5 0.10 10 LYD364 68018.4 — — — 8.10.22 14 0.5 0.12 9 LYD364 68020.5 — — — 9.8 L 37 0.5 0.03 12 LYD36468022.1 — — — 8.3 0.15 16 — — — LYD360 68061.1 — — — 8.7 0.06 22 0.50.02 12 LYD360 68061.2 — — — — — — 0.5 0.26 6 LYD360 68063.2 — — — — — —0.5 0.24 6 LYD357 68228.1 — — — — — — 0.5 0.13 8 LYD354 68133.4 — — —8.2 0.22 14 — — — LYD354 68133.6 — — — 8.0 0.29 12 — — — LYD354 68134.8— — — 8.2 0.21 15 — — — LYD349 68085.5 — — — 10.3 L 45 0.5 0.02 12LYD308 66881.2 — — — 8.4 0.12 18 — — — LYD295 67972.2 — — — 8.5 0.11 190.5 0.03 12 LYD295 67972.4 — — — 8.2 0.18 15 — — — CONT. — 0.6 — — 7.1 —— 0.5 — — LYD513 67217.3 — — — 6.0 0.05 22 0.4 0.06 10 LYD512 67209.1 —— — 5.6 0.26 13 0.3 0.28 7 LYD512 67209.4 — — — — — — 0.3 0.27 6 LYD48267334.1 — — — — — — 0.3 0.28 6 LYD475 67204.4 — — — 5.9 0.08 19 0.4 0.0411 LYD472 67332.1 — — — 6.1 0.04 23 0.4 0.05 11 LYD472 67332.3 — — — — —— 0.3 0.26 7 LYD472 67332.4 — — — 6.1 0.04 23 0.3 0.14 8 LYD466 67121.1— — — 5.9 0.07 20 0.4 0.06 10 LYD451 67187.7 — — — — — — 0.3 0.19 7LYD451 67188.1 — — — 5.8 0.13 18 0.4 0.02 14 LYD451 67188.4 — — — 5.80.12 17 0.3 0.26 6 LYD445 67353.2 — — — 5.6 0.19 14 0.3 0.26 6 LYD43967094.1 — — — 5.5 0.26 12 0.3 0.23 8 LYD439 67094.3 — — — 5.8 0.12 180.3 0.13 8 LYD439 67095.6 — — — 5.6 0.22 13 — — — LYD415 67266.6 — — — —— — 0.3 0.27 7 LYD382 67174.1 — — — 5.6 0.20 14 — — — LYD382 67175.2 — —— 5.7 0.15 16 — — — LYD382 67176.3 — — — — — — 0.3 0.14 9 LYD324 67167.1— — — — — — 0.3 0.23 7 LYD321 67280.1 — — — — — — 0.3 0.24 7 LYD32167283.1 — — — 5.8 0.10 18 0.4 0.09 9 LYD321 67283.3 — — — — — — 0.4 0.0810 LYD321 67283.4 — — — 6.8 L 37 0.4 L 16 LYD302 67414.3 — — — 5.6 0.2213 0.3 0.17 7 LYD302 67416.3 — — — 5.6 0.20 14 0.4 0.09 9 LYD296 67358.6— — — 6.1 0.05 23 0.4 0.07 12 LYD296 67359.3 — — — — — — 0.3 0.25 6LYD296 67360.1 — — — — — — 0.3 0.27 6 CONT. — — — — 4.9 — — 0.3 — —LYD517 67222.1 — — — 4.1 0.30 15 0.3 0.19 11 LYD515 67151.1 — — — 4.20.20 18 0.4 0.11 12 LYD515 67151.4 — — — — — — 0.3 0.30 8 LYD515 67152.4— — — 4.7 0.04 31 0.4 0.05 15 LYD502 67341.5 — — — 4.1 0.30 15 0.3 0.219 LYD498 67252.3 — — — 4.2 0.20 18 0.3 0.20 9 LYD498 67254.3 — — — 4.20.20 18 0.4 0.07 14 LYD492 67364.5 — — — — — — 0.3 0.28 8 LYD454 67192.5— — — 4.2 0.19 19 — — — LYD450 67178.3 — — — 4.1 0.29 15 — — — LYD45067182.2 — — — 4.2 0.18 19 0.3 0.25 9 LYD397 67324.2 — — — 4.6 0.05 290.4 0.08 14 LYD323 67286.1 — — — 4.2 0.23 17 0.3 0.20 9 LYD323 67287.3 —— — 4.2 0.22 18 0.3 0.24 9 LYD323 67288.2 — — — 4.2 0.28 18 — — — LYD31267256.4 — — — 4.6 0.05 30 0.3 0.21 9 LYD312 67256.5 — — — 4.2 0.24 17 —— — LYD301 67347.2 — — — 4.5 0.06 28 0.4 0.01 20 LYD298 66964.4 — — —4.4 0.08 25 0.4 0.07 13 LYD298 66966.2 — — — 4.1 0.29 15 — — — CONT. — —— — 3.6 — — 0.3 — — LYD508 67824.3 — — — 5.8 0.11 19 — — — LYD47967727.4 — — — 6.3 0.03 28 0.3 0.10 16 LYD428 67473.3 0.8 0.20 17 6.40.02 31 0.3 0.07 17 LYD346 67606.2 — — — 5.6 0.29 14 — — — CONT. — 0.6 —— 4.9 — — 0.3 — — LYD470 67126.7 — — — 8.7 0.15 19 0.4 0.02 12 LYD45967116.4 — — — — — — 0.4 0.24 6 LYD387 67316.1 — — — — — — 0.4 0.12 9LYD387 67317.4 0.8 0.25 12 9.3 0.04 26 0.4 L 15 LYD347 67848.2 — — — — —— 0.4 0.15 7 LYD338 67442.3 — — — 9.0 0.09 22 0.4 0.02 12 LYD337 66995.4— — — — — — 0.4 0.07 10 LYD337 66995.5 — — — — — — 0.4 0.10 8 LYD32266884.1 — — — — — — 0.4 0.24 6 LYD322 66884.2 — — — 8.4 0.26 14 0.4 0.177 LYD322 66886.6 — — — — — — 0.4 0.12 8 LYD322 66887.1 — — — — — — 0.40.12 8 LYD307 66975.3 — — — — — — 0.4 0.11 8 LYD307 66975.4 — — — — — —0.4 0.25 6 LYD307 66976.3 — — — — — — 0.4 0.12 8 LYD307 66977.3 — — —8.6 0.17 17 0.4 0.06 10 LYD303 67298.1 — — — — — — 0.4 0.20 7 LYD30367300.6 — — — — — — 0.4 0.19 7 CONT. — 0.7 — — 7.4 — — 0.4 — — LYD41067546.3 0.8 0.22 14 — — — — — — LYD379 67678.1 — — — 6.1 0.29 12 0.30.25 9 CONT. — 0.7 — — 5.5 — — 0.3 — — LYD489 67787.3 0.7 0.14 24 — — —— — — LYD483 68054.4 0.6 0.29 16 — — — — — — LYD471 68050.2 0.7 0.20 22— — — — — — LYD456 67964.1 0.7 0.22 21 — — — — — — LYD456 67967.4 0.60.24 19 — — — 0.5 0.17 11 LYD423 68218.3 0.7 0.09 26 — — — — — — LYD42268103.4 — — — 7.3 0.28 13 — — — LYD392 68033.3 — — — 7.7 0.13 19 — — —LYD365 68092.5 0.6 0.24 19 7.7 0.13 19 0.5 0.14 12 LYD359 67949.4 0.70.19 22 — — — — — — LYD351 68126.2 — — — 7.4 0.24 14 — — — LYD30666971.1 — — — 7.4 0.21 15 — — — LYD299 68115.7 — — — 7.6 0.15 18 0.50.28 8 CONT. — 0.5 — — 6.5 — — 0.4 — — LYD506 67144.2 0.8 0.25 10 8.30.10 22 0.4 0.25 9 LYD506 67146.2 — — — 8.5 0.07 24 — — — LYD504 67136.2— — — 7.8 0.26 14 — — — LYD504 67136.3 0.8 0.09 16 8.6 0.06 25 0.4 0.1711 LYD504 67139.1 — — — 8.4 0.08 23 0.4 0.18 11 LYD442 67104.3 — — — 8.60.06 26 — — — LYD440 66902.1 — — — 8.1 0.16 19 — — — LYD440 66902.2 — —— 8.0 0.23 16 0.4 0.26 9 LYD440 66906.1 — — — 8.2 0.15 20 — — — LYD43267959.2 — — — 8.5 0.08 24 0.4 0.27 9 LYD432 67961.2 — — — 8.3 0.12 21 —— — LYD425 67454.3 0.8 0.22 11 7.8 0.25 14 — — — LYD425 67454.5 — — —8.0 0.21 16 — — — LYD408 67304.1 0.8 0.21 12 9.1 0.02 33 0.4 0.21 10LYD408 67305.6 — — — 9.0 0.02 32 — — — LYD401 67086.2 — — — 7.8 0.27 14— — — LYD375 67070.2 — — — 8.0 0.19 17 — — — LYD375 67073.2 — — — 8.10.16 19 — — — LYD342 67059.4 — — — 7.9 0.22 16 — — — LYD342 67062.1 — —— 8.9 0.03 30 — — — LYD329 67277.4 — — — 8.0 0.18 17 — — — LYD32067040.2 0.8 0.28 11 — — — — — — LYD318 66980.7 — — — 7.8 0.29 14 — — —LYD318 66982.1 — — — 7.9 0.25 15 — — — LYD318 66983.4 — — — 8.6 0.06 25— — — LYD316 67436.1 0.8 0.11 15 8.1 0.17 18 — — — LYD316 67437.2 — — —8.1 0.18 18 0.4 0.29 8 LYD316 67439.1 0.8 0.15 14 8.5 0.07 24 — — —LYD298 66963.4 0.9 0.07 18 7.9 0.28 15 — — — LYD292 66998.3 — — — 8.40.09 22 — — — LYD292 66999.2 — — — 9.2 0.01 34 0.4 0.26 9 LYD292 66999.4— — — 8.0 0.21 17 — — — LYD292 67000.1 — — — 9.3 0.01 36 0.4 0.27 9CONT. — 0.7 — — 6.9 — — 0.4 — — Table 58. “CONT.”—Control;“Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L—p < 0.01.RGR = relative growth rate. The transgenes were under thetranscriptional regulation of the new At6669 promoter (SEQ ID NO:14467). “—“ = results are still unavailable.

TABLE 59 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Gene Harvest IndexRosette Area [cm²] Rosette Diameter [cm] Name Event # Ave. P-Val. %Incr. Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD446 68109.4 — — — — — —5.0 0.26 8 LYD446 68110.1 — — — 7.9 0.03 18 4.9 0.03 6 LYD443 68163.1 —— — 7.8 0.14 17 5.0 0.13 8 LYD443 68164.2 — — — 8.0 0.12 20 5.0 L 7LYD443 68165.3 — — — 7.9 L 18 5.1 L 9 LYD436 68073.3 — — — 8.0 0.02 215.0 L 6 LYD416 67904.3 — — — 7.1 0.03 6 4.7 0.29 1 LYD416 67907.6 — — —— — — 4.7 0.24 1 LYD391 68156.4 — — — 7.2 L 9 4.8 0.12 3 LYD391 68160.4— — — 8.6 0.09 28 5.3 0.14 13 LYD388 68096.2 — — — 7.9 L 19 5.0 L 8LYD388 68098.2 — — — 8.6 L 29 5.2 L 12 LYD388 68098.3 — — — 7.2 0.14 94.9 0.22 5 LYD388 68098.4 — — — — — — 5.1 0.17 9 LYD367 68066.5 — — —8.6 0.14 29 5.2 0.07 11 LYD364 68018.4 — — — 7.5 0.03 13 4.9 0.06 5LYD364 68020.1 — — — 6.9 0.29 3 — — — LYD364 68020.5 — — — 9.1 L 36 5.2L 12 LYD364 68022.1 — — — 7.8 0.15 17 4.9 0.16 6 LYD361 68147.1 — — —7.0 0.25 5 — — — LYD360 68061.1 — — — 8.1 0.02 22 5.2 0.03 11 LYD36068063.2 — — — 7.3 0.26 9 4.8 0.12 3 LYD357 68228.1 — — — 7.2 0.20 8 4.8L 4 LYD354 68133.4 — — — 7.7 0.11 16 4.9 0.29 5 LYD349 68085.3 — — — — —— 4.7 0.14 2 LYD349 68085.5 — — — 9.6 0.08 44 5.3 0.04 14 LYD308 66881.2— — — 7.9 0.02 18 4.9 0.02 5 LYD295 67972.2 — — — 7.9 0.17 18 5.0 0.02 8LYD295 67972.4 — — — 7.7 0.20 16 4.9 0.22 6 CONT. — — — — 6.7 — — 4.7 —— LYD513 67217.3 — — — 6.2 L 22 4.3 0.04 10 LYD512 67209.1 — — — — — —4.2 0.24 8 LYD482 67334.1 — — — — — — 4.2 0.24 7 LYD482 67335.3 — — — —— — 4.0 0.24 3 LYD482 67336.1 — — — — — — 4.1 0.23 4 LYD475 67202.3 — —— — — — 4.1 0.21 6 LYD475 67204.4 — — — 6.0 L 18 4.2 0.03 9 LYD47267332.1 — — — 6.2 0.06 23 4.3 0.03 10 LYD472 67332.3 — — — — — — 4.20.21 7 LYD472 67332.4 — — — 6.2 L 23 4.4 L 11 LYD466 67121.1 — — — 6.1 L21 4.3 L 11 LYD452 67106.2 — — — 5.4 0.20 7 — — — LYD451 67187.9 — — —5.5 0.09 8 — — — LYD451 67188.1 — — — — — — 4.3 0.20 9 LYD451 67188.4 —— — 5.9 0.07 17 4.1 0.12 6 LYD445 67353.1 — — — 5.4 0.27 7 — — — LYD44567353.2 — — — 5.9 L 16 4.2 0.01 8 LYD445 67354.5 — — — 5.3 0.29 6 — — —LYD439 67094.1 — — — — — — 4.2 0.22 7 LYD439 67094.3 — — — 5.9 0.06 174.2 0.03 8 LYD439 67095.2 — — — — — — 4.1 0.16 6 LYD439 67095.6 — — —5.7 0.02 13 4.2 0.02 6 LYD415 67262.1 — — — 5.6 0.21 11 4.2 L 8 LYD41567264.5 — — — 5.4 0.13 7 4.0 0.21 3 LYD382 67174.1 — — — 5.7 0.19 13 — —— LYD382 67175.2 — — — 5.9 0.16 17 4.2 0.05 7 LYD382 67176.3 — — — — — —4.2 0.06 7 LYD339 67247.3 — — — — — — 4.0 0.25 2 LYD324 67167.1 — — — —— — 4.1 0.30 4 LYD321 67283.1 — — — 6.0 0.01 18 4.2 0.07 8 LYD32167283.3 — — — — — — 4.2 0.13 6 LYD321 67283.4 — — — 6.9 0.04 36 4.6 0.0319 LYD302 67414.3 — — — 5.8 0.03 14 4.2 L 8 LYD302 67416.3 — — — 5.70.02 12 4.2 0.02 7 LYD296 67358.6 — — — 6.3 0.14 24 4.4 0.24 12 LYD29667359.3 — — — — — — 4.2 0.01 7 LYD296 67360.1 — — — — — — 4.1 0.08 5CONT. — — — — 5.1 — — 3.9 — — LYD517 67221.3 — — — 3.8 0.14 6 3.6 0.03 7LYD517 67221.5 — — — — — — 3.4 0.29 3 LYD515 67151.1 — — — 4.2 0.08 173.8 0.02 12 LYD515 67151.4 — — — — — — 3.7 0.28 9 LYD515 67151.6 — — — —— — 3.6 0.05 7 LYD515 67152.4 — — — 4.6 L 29 3.8 0.03 14 LYD502 67340.4— — — 4.0 0.09 13 3.6 0.12 6 LYD502 67341.5 — — — 4.1 0.04 15 3.7 0.0210 LYD502 67342.6 — — — 3.9 0.02 11 3.5 0.09 5 LYD498 67252.3 — — — 4.2L 17 3.7 0.01 9 LYD498 67254.1 — — — 3.9 0.06 10 3.5 0.06 6 LYD49867254.3 — — — 4.1 0.01 16 3.7 L 10 LYD492 67364.5 — — — 3.9 0.20 11 3.60.20 7 LYD474 67199.1 — — — 3.9 0.05 9 — — — LYD454 67192.5 — — — 4.20.02 18 3.6 0.02 9 LYD450 67178.3 — — — 4.1 0.02 14 3.6 0.07 7 LYD45067180.2 — — — 4.0 0.27 11 3.6 0.18 7 LYD450 67182.2 — — — 4.2 0.01 183.7 0.06 10 LYD428 67472.2 — — — — — — 3.5 0.11 5 LYD397 67322.1 — — —3.8 0.28 6 — — — LYD397 67324.2 — — — 4.5 0.04 28 3.8 L 14 LYD32367286.1 — — — 4.1 0.29 16 3.7 0.08 9 LYD323 67287.3 — — — 4.1 L 16 3.60.02 7 LYD312 67256.4 — — — 4.6 0.08 30 3.8 0.09 13 LYD312 67256.5 — — —4.1 L 16 3.6 0.02 7 LYD310 67161.1 — — — 4.0 0.04 12 3.5 0.29 3 LYD31067164.1 — — — 3.8 0.08 7 3.5 0.22 3 LYD301 67347.2 — — — 4.4 0.01 25 3.80.05 14 LYD301 67347.4 — — — 4.0 0.13 12 3.6 0.08 6 LYD298 66964.4 — — —4.4 0.15 24 3.8 0.01 14 LYD298 66966.2 — — — 4.1 L 15 3.6 0.02 7 CONT. —— — — 3.5 — — 3.4 — — LYD508 67823.1 0.4 0.23 14 — — — — — — LYD50867823.2 0.4 0.29 7 5.6 0.13 7 4.0 0.23 2 LYD508 67823.4 0.4 0.14 11 — —— — — — LYD508 67824.3 — — — 6.2 0.08 18 4.2 0.11 6 LYD503 67526.2 0.40.08 17 — — — — — — LYD503 67529.1 0.4 0.24 7 — — — — — — LYD503 67529.30.4 0.27 8 — — — — — — LYD497 67880.3 0.4 0.30 8 — — — — — — LYD49767883.4 — — — 5.8 0.03 10 4.1 0.08 5 LYD491 67876.2 0.4 0.29 20 — — — —— — LYD489 67787.4 0.4 0.16 9 — — — — — — LYD479 67727.4 — — — 6.7 0.2128 4.4 L 12 LYD458 67922.2 0.4 0.29 11 — — — — — — LYD435 67707.3 0.40.14 9 — — — — — — LYD435 67708.2 0.4 0.03 15 — — — — — — LYD433 67700.10.4 0.04 21 — — — — — — LYD433 67704.4 0.4 0.19 9 — — — — — — LYD42867473.3 0.4 0.07 12 6.8 L 29 4.4 L 12 LYD428 67474.3 0.4 0.08 14 — — — —— — LYD305 67535.5 0.4 0.29 7 — — — — — — CONT. — 0.4 — — 5.2 — — 3.9 —— LYD484 67135.3 — — — 8.1 0.05 6 4.9 0.20 3 LYD470 67126.7 — — — 9.1 L20 5.2 0.04 9 LYD470 67127.3 — — — 7.7 0.25 2 4.8 0.20 2 LYD459 67116.4— — — — — — 4.9 0.02 3 LYD387 67317.4 — — — 9.4 0.06 24 5.4 L 14 LYD33867442.3 — — — 9.2 0.12 21 5.3 L 11 LYD337 66994.3 — — — 7.8 0.12 4 — — —LYD337 66995.4 — — — — — — 5.0 0.27 5 LYD337 66995.5 — — — 8.2 0.23 8 —— — LYD322 66884.1 — — — — — — 4.9 0.03 3 LYD322 66884.2 — — — 8.6 L 135.0 L 5 LYD322 66886.6 — — — — — — 4.9 0.04 4 LYD322 66887.1 — — — 8.30.02 9 5.0 0.13 5 LYD307 66975.3 — — — 8.1 0.05 7 4.9 0.02 4 LYD30766975.4 — — — — — — 4.9 0.11 2 LYD307 66977.3 — — — 8.7 0.13 15 5.1 0.218 CONT. — — — — 7.6 — — 4.7 — — LYD453 67484.1 0.4 0.07 12 — — — — — —LYD453 67485.2 0.4 0.07 11 — — — — — — LYD453 67485.5 0.4 0.10 15 — — —— — — LYD410 67546.1 0.4 0.25 6 — — — — — — LYD410 67548.3 0.4 0.08 11 —— — — — — LYD409 67468.2 0.4 0.29 8 — — — — — — LYD409 67469.1 0.4 0.295 — — — — — — LYD405 67694.4 0.4 0.12 9 — — — — — — LYD405 67695.2 0.5 L22 — — — — — — LYD405 67696.2 0.4 0.02 16 — — — — — — LYD405 67697.2 0.40.16 7 — — — — — — LYD404 67690.2 0.4 0.18 8 — — — — — — LYD404 67690.40.4 0.24 16 — — — — — — LYD403 67770.3 0.4 0.20 7 — — — — — — LYD40267762.1 0.4 0.19 8 — — — — — — LYD402 67765.3 0.4 0.21 7 — — — — — —LYD396 67754.1 0.4 0.11 17 — — — — — — LYD396 67759.3 0.4 0.04 17 — — —— — — LYD379 67678.1 — — — 6.4 0.13 11 4.2 0.02 5 LYD372 67673.4 — — — —— — 4.1 0.12 3 LYD366 67810.4 0.4 0.19 16 — — — — — — LYD366 67812.1 0.40.12 8 — — — — — — LYD362 67538.2 0.4 0.03 13 — — — — — — LYD362 67543.50.4 0.29 6 — — — — — — LYD362 67543.6 0.4 0.01 19 — — — — — — LYD35567641.3 0.4 0.02 15 — — — — — — LYD355 67641.4 0.4 0.11 9 — — — — — —LYD355 67643.3 0.4 0.05 12 — — — — — — LYD348 67851.6 0.4 0.25 6 — — — —— — LYD348 67851.7 0.4 L 18 — — — — — — LYD348 67853.1 0.5 0.08 24 — — —— — — LYD348 67854.3 0.4 0.02 16 — — — — — — LYD347 67844.2 0.4 0.10 9 —— — — — — LYD347 67848.2 0.4 0.10 9 — — — — — — CONT. — 0.4 — — 5.7 — —4.0 — — LYD489 67785.4 — — — 6.5 0.18 6 — — — LYD472 67332.4 — — — 6.70.18 10 — — — LYD458 67922.1 — — — — — — 4.6 0.27 3 LYD456 67966.3 — — —6.7 0.06 8 4.7 0.14 4 LYD456 67967.4 — — — 6.4 0.14 5 4.7 0.18 4 LYD42268103.3 — — — — — — 4.7 0.15 4 LYD417 68045.3 — — — — — — 4.6 0.28 3LYD392 68032.2 — — — 6.7 0.21 8 4.7 0.09 6 LYD392 68033.3 — — — 7.3 L 184.8 0.14 6 LYD365 68092.4 — — — 6.6 0.13 7 4.6 0.26 3 LYD365 68092.5 — —— 7.2 0.22 18 4.9 0.01 9 LYD365 68093.2 — — — 6.7 0.17 8 4.7 0.27 4LYD359 67946.3 — — — 6.5 0.29 5 — — — LYD351 68126.2 — — — 7.0 L 13 4.70.09 5 LYD351 68129.5 — — — 6.5 0.14 6 — — — LYD306 66971.1 — — — 7.0 L14 4.8 0.06 6 LYD299 68115.7 — — — 7.2 L 17 4.8 0.04 7 CONT. — — — — 6.2— — 4.5 — — LYD506 67144.2 — — — 8.4 0.01 19 5.1 L 9 LYD506 67146.2 — —— 8.8 0.10 24 5.1 0.28 9 LYD504 67136.2 — — — 7.9 0.04 12 4.9 0.06 5LYD504 67136.3 — — — 8.7 L 23 5.1 L 10 LYD504 67138.1 — — — 7.8 0.16 11— — — LYD504 67139.1 — — — 8.6 0.02 22 5.1 0.02 10 LYD504 67140.1 — — —7.7 0.13 9 4.8 0.27 3 LYD466 67119.4 — — — 7.6 0.24 8 — — — LYD44267104.3 — — — 8.7 0.20 23 5.1 0.17 9 LYD440 66902.1 — — — 8.3 0.08 175.0 0.03 6 LYD440 66902.2 — — — 8.2 0.08 16 5.0 0.04 6 LYD440 66906.1 —— — 8.4 L 19 5.0 0.03 7 LYD432 67959.2 — — — 8.6 0.22 22 5.1 0.22 9LYD432 67961.2 — — — 8.4 L 19 5.1 0.10 9 LYD425 67454.3 — — — 7.9 0.0511 4.9 0.07 5 LYD425 67454.5 — — — 8.1 0.15 15 4.9 0.22 5 LYD408 67304.1— — — 9.3 L 32 5.2 0.01 12 LYD408 67305.6 — — — 9.3 0.07 32 5.3 L 14LYD408 67306.2 — — — 7.9 0.09 12 — — — LYD401 67084.2 — — — 7.6 0.17 84.8 0.27 3 LYD401 67086.2 — — — — — — 4.9 0.19 6 LYD375 67070.2 — — —8.0 0.05 13 4.9 0.05 5 LYD375 67073.2 — — — 8.2 0.03 17 5.0 0.03 7LYD342 67059.4 — — — 8.0 0.03 13 4.9 0.05 5 LYD342 67062.1 — — — 9.1 L28 5.1 L 9 LYD329 67275.1 — — — 7.5 0.26 6 — — — LYD329 67277.4 — — —8.2 0.04 16 5.0 0.25 7 LYD320 67040.2 — — — 7.5 0.24 6 — — — LYD32067043.1 — — — 7.5 0.20 6 4.8 0.14 4 LYD318 66980.3 — — — 7.6 0.14 8 4.90.12 5 LYD318 66980.5 — — — 7.8 0.08 11 4.8 0.17 4 LYD318 66982.1 — — —8.0 0.03 13 4.9 0.17 4 LYD318 66983.4 — — — 8.8 L 25 5.1 L 10 LYD31667436.1 — — — 8.1 0.02 14 4.9 0.19 5 LYD316 67437.2 — — — 8.1 0.02 155.0 0.10 8 LYD316 67439.1 — — — 8.7 L 23 5.1 0.02 10 LYD311 67425.1 — —— — — — 4.8 0.27 4 LYD292 66998.3 — — — 8.5 L 21 5.0 0.02 7 LYD29266999.2 — — — 9.3 0.05 32 5.3 L 13 LYD292 66999.4 — — — 8.1 0.14 15 — —— LYD292 67000.1 — — — 9.5 0.01 34 5.2 0.04 11 CONT. — — — — 7.1 — — 4.7— — Table 59. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment;“p-val.”—p-value, L—p < 0.01. The transgenes were under thetranscriptional regulation of the new At6669 promoter (SEQ ID NO:14467). “—“ = results are still unavailable.

TABLE 60 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Seed 1000 Seed Yield [mg]Weight [mg] Gene Event P- % P- % Name # Ave. Val. Incr. Ave. Val. Incr.LYD508 67823.2 459.9 0.08 18 — — — LYD508 67823.4 432.1 0.24 11 — — —LYD508 67824.3 455.4 0.08 17 — — — LYD503 67529.1 430.3 0.25 10 — — —LYD503 67529.3 417.3 0.13 7 — — — LYD497 67883.1 427.1 0.08 9 — — —LYD489 67784.4 413.4 0.18 6 — — — LYD435 67706.1 426.1 0.11 9 — — —LYD435 67708.1 417.9 0.24 7 — — — LYD433 67700.1 487.3 0.01 25 — — —LYD433 67704.4 435.2 0.11 11 — — — LYD428 67473.3 494.4 0.06 27 — — —LYD428 67474.3 444.4 0.20 14 — — — LYD346 67605.4 444.8 0.06 14 — — —CONT. — 390.4 — — — — — LYD453 67485.2 454.1 0.13 7 — — — LYD410 67546.3454.3 0.06 7 — — — LYD409 67468.2 490.5 0.18 15 — — — LYD405 67695.2511.4 0.02 20 — — — LYD405 67696.2 534.5 0.28 26 — — — LYD396 67759.5483.5 L 14 — — — LYD379 67677.1 476.9 0.19 12 — — — LYD366 67812.5 478.30.14 12 — — — LYD362 67538.2 499.0 L 17 — — — LYD355 67641.3 470.8 0.0811 — — — LYD348 67851.7 476.1 0.01 12 — — — LYD348 67853.1 519.8 0.18 22— — — LYD348 67854.3 472.8 0.29 11 — — — LYD347 67844.2 497.9 L 17 — — —CONT. — 425.5 — — — — — ″CONT.″—Control; ″Ave.″—Average; ″% Incr.″ = %increment; ″p-val.″—p-value, L—p < 0.01. The transgenes were under thetranscriptional regulation of the new At6669 promoter (SEQ ID NO:14467). “—“ = results are still unavailable.

Example 17 Evaluation of Transgenic Arabidopsis for Seed Yield and PlantGrowth Rate Under Normal Conditions in Greenhouse Assays Until Bolting(GH-SB Assays)

Assay 2: Plant performance improvement measured until bolting stage:plant biomass and plant growth rate under normal greenhouse conditions(GH-SB Assays)—This assay follows the plant biomass formation and therosette area growth of plants grown in the greenhouse under normalgrowth conditions. Transgenic Arabidopsis seeds were sown in agar mediasupplemented with % MS medium and a selection agent (Kanamycin). The T2transgenic seedlings were then transplanted to 1.7 trays filled withpeat and perlite in a 1:1 ratio. The trays were irrigated with asolution containing of 6 mM inorganic nitrogen in the form of KNO₃ with1 mM KH₂PO₄, 1 mM MgSO₄. 2 mM CaCl₂) and microelements. All plants weregrown in the greenhouse until bolting stage. Plant biomass (the aboveground tissue) was weight in directly after harvesting the rosette(plant fresh weight [FW]). Following plants were dried in an oven at 50°C. for 48 hours and weighted (plant dry weight [DW]).

Each construct was validated at its T₂ generation. Transgenic plantstransformed with a construct conformed by an empty vector carrying the35S promoter and the selectable marker was used as control.

The plants were analyzed for their overall size, growth rate, freshweight and dry matter. Transgenic plants performance was compared tocontrol plants grown in parallel under the same conditions.Mock-transgenic plants expressing the uidA reporter gene (GUS-Intron) orwith no gene at all, under the same promoter were used as control.

The experiment was planned in nested randomized plot distribution. Foreach gene of the invention three to five independent transformationevents were analyzed from each construct.

Digital imaging—A laboratory image acquisition system, which consists ofa digital reflex camera (Canon EOS 300D) attached with a 55 mm focallength lens (Canon EF-S series), mounted on a reproduction device(Kaiser RS), which includes 4 light units (4×150 Watts light bulb) wasused for capturing images of plant samples.

The image capturing process was repeated every 2 days starting from day1 after transplanting till day 15. Same camera, placed in a custom madeiron mount, was used for capturing images of larger plants sawn in whitetubs in an environmental controlled greenhouse. The tubs were squareshape include 1.7 liter trays. During the capture process, the tubeswere placed beneath the iron mount, while avoiding direct sun light andcasting of shadows.

An image analysis system was used, which consists of a personal desktopcomputer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ1.39 [Java based image processing program which was developed at theU.S. National Institutes of Health and freely available on the internetat Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Imageswere captured in resolution of 10 Mega Pixels (3888×2592 pixels) andstored in a low compression JPEG (Joint Photographic Experts Groupstandard) format. Next, analyzed data was saved to text files andprocessed using the JMP statistical analysis software (SAS institute).

Leaf analysis—Using the digital analysis leaves data was calculated,including leaf number, rosette area, rosette diameter, and leaf bladearea.

Vegetative growth rate: the relative growth rate (RGR) of leaf number(Formula IX, described above), rosette area (Formula VIII describedabove) and plot coverage (Formula XIII, described above) were calculatedusing the indicated formulas.

Plant Fresh and Dry weight—On about day 80 from sowing, the plants wereharvested and directly weight for the determination of the plant freshweight (FW) and left to dry at 50° C. in a drying chamber for about 48hours before weighting to determine plant dry weight (DW).

Statistical analyses—To identify outperforming genes and constructs,results from the independent transformation events tested were analyzedseparately. Data was analyzed using Student's t-test and results areconsidered significant if the p value was less than 0.1. The JMPstatistics software package was used (Version 5.2.1, SAS Institute Inc.,Cary, N.C., USA).

Experimental Results:

Tables 61-64 summarize the observed phenotypes of transgenic plantsexpressing the genes constructs using the GH-SB Assays.

The genes listed in Tables 61-64 improved plant performance when grownat normal conditions. These genes produced larger plants with a largerphotosynthetic area, biomass (fresh weight, dry weight, rosettediameter, rosette area and plot coverage), relative growth rate, bladerelative area and petiole relative area. The genes were cloned under theregulation of a constitutive At6669 promoter (SEQ ID NO:14467). Theevaluation of each gene was performed by testing the performance ofdifferent number of events. Event with p-value <0.1 was consideredstatistically significant.

TABLE 61 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Dry Weight [mg] FreshWeight [mg] Leaf Number Gene Event P- % P- % P- % Name # Ave. Val. Incr.Ave. Val. Incr. Ave. Val Incr. LYD511 67774.3 426.2 0.21 7 — — — — — —LYD441 67714.3 — — — — — — 10.2 0.11 3 LYD410 67546.2 431.2 0.23 85181.2 0.14 7 — — — LYD410 67546.3 — — — — — — 10.6 0.13 7 LYD39667754.1 426.2 0.22 7 5081.2 0.25 5 10.6 0.14 7 LYD396 67759.3 453.8 0.2614 — — — — — — CONT. — 398.3 — — 4845.8 — — 9.9 — — LYD504 67136.2 — — —5918.8 0.02 8 10.8 0.03 3 LYD504 67140.1 383.1 0.15 6 — — — — — — LYD48467133.3 — — — 5720.5 0.19 4 — — — LYD478 67272.3 389.4 0.20 8 — — — 10.70.13 2 LYD470 67125.4 391.4 0.17 9 — — — — — — LYD470 67126.7 — — —5968.8 0.25 9 — — — LYD466 67118.1 — — — 5606.2 0.19 2 — — — LYD46667120.2 377.5 0.17 5 — — — — — — LYD442 67103.1 380.6 0.09 6 — — — — — —LYD440 66903.1 383.1 0.15 6 6168.8 L 13 11.2 0.14 8 LYD438 66899.2 — — —6087.5 0.23 11 11.1 0.27 6 LYD438 66900.3 379.4 0.28 5 — — — — — —LYD408 67305.6 373.8 0.24 4 — — — — — — LYD395 67080.6 — — — 5843.8 0.017 — — — LYD387 67317.1 389.4 0.03 8 — — — — — — LYD387 67317.4 — — — — —— 10.9 0.08 4 LYD385 66891.2 — — — 5762.5 0.04 5 — — — LYD385 66893.1 —— — 5850.0 L 7 — — — LYD375 67070.2 — — — 5818.8 0.10 6 — — — LYD37567070.3 383.8 0.19 6 5756.2 0.18 5 — — — LYD375 67071.4 — — — 6281.20.18 15 — — — LYD342 67063.2 — — — 5937.5 0.11 8 — — — LYD330 67046.2417.5 L 16 5912.5 0.17 8 11.1 0.27 6 LYD330 67050.2 — — — — — — 11.1 L 6LYD330 67050.5 — — — — — — 10.7 0.13 2 LYD329 67277.4 373.1 0.29 35700.0 0.04 4 — — — LYD325 67015.4 373.1 0.29 3 — — — — — — LYD32266884.2 — — — 5700.0 0.19 4 — — — LYD320 67043.1 — — — 5706.2 0.28 4 — —— LYD320 67044.2 — — — 5748.8 0.02 5 — — — LYD318 66983.4 409.4 0.04 146275.0 0.15 15 — — — LYD315 67004.4 — — — — — — 11.3 0.06 8 LYD31567005.2 — — — 5656.2 0.25 3 — — — LYD315 67007.4 413.8 0.04 15 5875.00.26 7 11.3 0.06 8 LYD298 66962.3 382.0 0.20 6 — — — — — — LYD29366957.2 — — — 5793.8 L 6 — — — LYD292 66998.3 413.1 0.11 15 6712.5 L 23— — — LYD292 67000.1 380.6 0.09 6 6362.5 0.10 16 — — — CONT. — 360.6 — —5474.6 — — 10.5 — — LYD471 68050.2 353.8 0.05 26 4675.0 0.10 25 — — —LYD471 68050.4 — — — 4656.2 0.15 25 9.8 0.10 4 LYD446 68109.4 — — —4143.8 0.17 11 — — — LYD446 68110.1 — — — 3943.8 0.28 6 9.7 0.30 4LYD446 68110.3 302.5 0.24 8 4593.8 0.10 23 — — — LYD446 68111.4 — — — —— — 9.8 0.15 4 LYD432 67959.2 — — — 3937.5 0.30 6 — — — LYD432 67960.6 —— — — — — 9.8 0.18 5 LYD422 68102.3 — — — 4537.5 0.23 22 9.7 0.16 4LYD422 68103.3 366.9 0.29 31 4587.5 0.01 23 — — — LYD417 68043.1 315.00.09 12 4487.5 0.27 20 — — — LYD417 68043.3 — — — 4065.2 0.17 9 — — —LYD417 68043.5 302.5 0.28 8 — — — — — — LYD385 66891.2 305.0 0.21 94306.2 0.04 15 — — — LYD385 66891.3 — — — — — — 9.9 0.07 6 LYD36867661.1 324.4 0.23 16 4050.0 0.21 9 — — — LYD364 68018.3 — — — 4137.50.07 11 — — — LYD364 68020.1 306.9 0.17 9 — — — — — — LYD364 68020.2 — —— — — — 9.8 0.18 5 LYD351 68129.3 — — — 4131.2 0.09 11 — — — LYD34468123.2 — — — 4400.0 0.08 18 — — — LYD335 67557.5 — — — — — — 9.7 0.16 4LYD330 67047.8 — — — 4156.2 0.09 11 9.7 0.16 4 LYD315 67004.4 — — — — —— 9.7 0.16 4 LYD315 67007.4 362.5 0.29 29 4312.5 0.24 16 — — — LYD30967421.4 — — — — — — 9.8 0.18 5 LYD308 66880.2 331.2 0.03 18 4075.0 0.119 — — — LYD299 68114.6 — — — — — — 9.6 0.29 3 LYD299 68115.4 — — —4331.2 0.02 16 — — — LYD299 68115.6 339.4 0.01 21 4056.3 0.28 9 — — —LYD299 68115.7 — — — 4006.2 0.17 7 — — — LYD299 68118.5 347.5 0.24 244537.5 L 22 — — — CONT. — 280.6 — — 3731.2 — — 9.4 — — LYD517 67221.3508.8 0.20 10 7375.0 0.03 8 — — — LYD517 67221.5 493.8 0.09 7 7412.50.03 9 — — — LYD517 67222.1 503.1 0.08 9 7550.0 L 11 — — — LYD51567151.1 517.5 0.05 12 8000.0 0.08 18 — — — LYD515 67151.4 512.5 0.12 117343.8 0.12 8 — — — LYD515 67151.6 — — — 7612.5 L 12 — — — LYD51267209.1 485.0 0.16 5 7556.2 0.24 11 — — — LYD512 67211.4 509.4 0.02 117362.5 0.03 8 — — — LYD512 67212.2 501.2 0.04 9 7331.2 0.04 8 — — —LYD502 67342.6 490.0 0.18 6 7381.2 0.03 8 — — — LYD498 67254.3 488.80.11 6 7081.2 0.25 4 — — — LYD492 67364.5 512.5 0.15 11 7468.8 0.14 10 —— — LYD482 67334.1 506.9 0.03 10 7637.5 L 12 — — — LYD475 67204.2 — — —7437.5 0.23 9 — — — LYD475 67204.4 — — — 7681.2 0.26 13 — — — LYD45467192.5 523.8 0.01 14 7275.0 0.25 7 — — — LYD454 67193.4 — — — 7387.50.12 9 — — — LYD452 67106.2 545.0 0.09 18 7637.5 0.11 12 — — — LYD45167187.7 483.1 0.24 5 7112.5 0.19 5 — — — LYD451 67188.4 534.4 0.04 167893.8 0.08 16 10.2 0.07 5 LYD450 67182.2 — — — 7425.0 0.25 9 — — —LYD445 67353.1 — — — 7325.0 0.08 8 — — — LYD439 67094.1 — — — — — — 10.10.17 4 LYD439 67096.1 — — — — — — 10.4 0.03 7 LYD415 67262.1 — — —7781.2 L 14 — — — LYD415 67266.1 — — — 7612.5 0.27 12 — — — LYD41567266.3 — — — 7681.2 L 13 — — — LYD415 67266.6 500.0 0.04 9 7393.8 0.229 — — — LYD399 67448.3 556.2 0.20 21 8118.8 L 19 10.7 0.02 10 LYD39767322.2 482.5 0.23 5 — — — — — — LYD397 67323.2 — — — 7225.0 0.13 6 — —— LYD339 67247.3 — — — — — — 10.0 0.23 3 LYD328 67238.2 491.9 0.10 7 — —— — — — LYD328 67242.1 512.5 0.30 11 7468.8 0.02 10 — — — LYD324 67168.4492.5 0.09 7 7143.8 0.15 5 — — — LYD323 67287.3 — — — 7087.5 0.23 4 — —— LYD323 67288.2 — — — 7662.5 0.29 13 — — — LYD321 67280.1 519.4 L 137356.2 0.07 8 — — — LYD321 67281.6 498.8 0.05 8 7331.2 0.29 8 — — —LYD321 67283.1 484.4 0.17 5 — — — — — — LYD321 67283.3 508.8 0.10 107300.0 0.25 7 — — — LYD316 67437.2 512.5 0.01 11 7412.5 0.07 9 — — —LYD316 67439.1 — — — 7356.2 0.11 8 — — — LYD312 67256.4 518.8 L 137868.8 L 16 — — — LYD312 67257.3 511.9 0.01 11 7293.8 0.05 7 — — —LYD310 67163.1 486.9 0.26 6 7343.8 0.04 8 — — — LYD310 67164.1 494.40.24 7 — — — 10.1 0.15 4 LYD309 67418.3 518.1 L 12 7737.5 0.02 14      LYD296 67359.1 515.0 0.01 12 7718.8 L 13 10.1 0.17 4 LYD291 67400.2529.1 0.17 15 7560.7 0.07 11 — — — LYD291 67400.5 — — — 7806.2 0.11 15 —— — LYD290 67233.3 — — — 7187.5 0.21 6 — — — LYD290 67233.5 — — — 7331.20.12 8 — — — LYD290 67236.4 — — — 7368.8 0.18 8 — — — CONT. — 460.8 — —6804.7 — — 9.7 — — LYD489 67785.4 — — — 5331.2 L 10 — — — LYD489 67787.4— — — 5093.8 0.22 5 — — — LYD458 67922.2 434.4 0.24 6 — — — — — — LYD45367484.1 436.9 0.07 6 — — — — — — LYD453 67485.1 — — — — — — 10.6 0.20 4LYD453 67487.2 — — — — — — 11.8 L 15 LYD448 67918.2 — — — 5168.8 0.16 710.6 0.15 4 LYD433 67700.1 — — — 5162.5 0.26 7 — — — LYD433 67704.4 — —— — — — 10.9 0.21 7 LYD409 67467.4 — — — 5193.8 0.05 7 — — — LYD40967468.1 — — — 5300.0 0.30 10 11.4 0.08 12 LYD404 67690.2 — — — 5464.60.13 13 — — — LYD403 67768.3 — — — 5087.5 0.16 5 — — — LYD403 67771.1 —— — 5375.0 0.16 11 — — — LYD402 67760.2 451.5 0.02 10 5151.8 0.05 6 — —— LYD402 67762.3 — — — — — — 11.1 0.02 9 LYD402 67765.3 — — — 5168.80.06 7 — — — LYD368 67659.1 — — — 5520.5 0.24 14 11.1 0.27 8 LYD36867659.5 460.6 0.23 12 — — — — — — LYD368 67661.1 — — — 5325.0 0.30 10 —— — LYD355 67640.1 — — — 5106.2 0.20 6 — — — LYD347 67844.2 — — — 5450.00.13 13 — — — LYD346 67605.4 — — — 5231.2 0.19 8 — — — CONT. — 411.0 — —4839.6 — — 10.2 — — LYD483 68054.3 264.4 0.16 13 3631.2 0.12 12 — — —LYD483 68054.4 256.2 0.14 9 3487.5 0.27 8 — — — LYD483 68056.4 265.00.06 13 — — — — — — LYD478 67268.1 — — — — — — 9.8 0.02 5 LYD478 67269.2265.6 0.05 13 3956.2 L 22 — — — LYD478 67270.1 — — — 3637.5 0.16 12 — —— LYD460 67930.1 286.2 L 22 — — — — — — LYD460 67930.3 — — — — — — 10.30.04 11 LYD423 68216.2 — — — 3600.0 0.23 11 — — — LYD423 68216.3 262.50.06 12 3600.0 0.10 11 — — — LYD423 68218.7 — — — 3768.8 0.03 16 — — —LYD395 67077.1 — — — 3806.2 0.14 18 — — — LYD395 67078.1 — — — — — — 9.80.14 6 LYD395 67080.6 — — — 3600.0 0.21 11 — — — LYD392 68032.2 257.50.11 10 — — — 9.6 0.13 3 LYD392 68033.3 — — — 3525.0 0.28 9 — — — LYD38868098.3 — — — — — — 9.6 0.13 3 LYD376 68024.2 — — — 3963.4 L 22 — — —LYD376 68025.1 — — — — — — 9.6 0.06 4 LYD376 68026.2 — — — 3637.5 0.0812 — — — LYD367 68066.5 270.0 0.18 15 3731.2 0.11 15 — — — LYD36768066.6 — — — 3550.0 0.18 10 — — — LYD367 68068.5 257.5 0.11 10 — — — —— — LYD365 68092.3 — — — 3556.2 0.23 10 — — — LYD365 68092.4 — — —3518.8 0.19 9 — — — LYD365 68092.5 — — — 3525.0 0.20 9 — — — LYD36168145.9 — — — — — — 9.6 0.13 3 LYD361 68146.7 255.0 0.14 9 3668.8 0.0713 — — — LYD361 68147.1 — — — — — — 9.9 0.20 6 LYD360 68061.2 — — — — —— 9.8 0.14 6 LYD360 68064.1 — — — — — — 9.6 0.13 3 LYD356 68139.2 — — —3737.5 0.04 15 9.6 0.13 3 LYD356 68140.3 — — — — — — 9.9 0.04 6 LYD35468133.6 — — — 3712.5 0.09 15 — — — LYD349 68084.1 — — — 3562.5 0.14 10 —— — LYD349 68085.5 — — — — — — 9.5 0.20 2 LYD349 68085.6 — — — — — — 9.60.15 4 LYD332 66988.1 321.2 L 37 3981.2 L 23 — — — LYD332 66989.2 286.2L 22 3700.0 0.05 14 — — — LYD325 67015.4 — — — 3506.2 0.20 8 — — —LYD297 67227.5 — — — — — — 9.8 0.14 6 CONT. — 234.6 — — 3237.5 — — 9.3 —— LYD434 67978.2 — — — — — — 9.7 0.22 3.1 LYD434 67977.3 — — — — — — 9.60.32 2.1 CONT. — — — — — — — 9.4 — — LYD305 67535.2 440.3 0.19 10 4865.80.84 1.2 — — — CONT. — 400.4 — — 4808.2 — — — — — LYD481 67778.1 471.20.07 18.3 — — — — — — LYD491 67874.3 428.1 0.45 7.5 — — — — — — LYD43567709.2 420.0 0.58 5.4 — — — — — — LYD481 67779.4 420.0 0.58 5.4 — — — —— — CONT. — 398.3 — — — — — — — — ″CONT.″—Control; ″Ave.″—Average; ″%Incr.″ = % increment; ″p-val.″—p-value, L—p < 0.01. The transgenes wereunder the transcriptional regulation of the new At6669 promoter (SEQ IDNO: 14467). “—“ = results are still unavailable.

TABLE 62 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Plot Coverage [cm²]Rosette Area [cm²] Rosette Diameter [cm] Gene Event P- P- P- Name # Ave.Val. Incr. Ave.. Val. Incr. Ave. Val. Incr. LYD479 67728.5 — — — — — —4.5 0.07 8 LYD396 67754.1 — — — — — — 4.5 0.27 6 CONT. — — — — — — — 4.2— — LYD504 67136.2 79.9 0.03 16 10.0 0.03 16 5.5 L 10 LYD484 67135.3 — —— — — — 5.2 0.15 4 LYD478 67269.2 79.6 L 15 10.0 L 15 5.5 L 11 LYD47867272.3 74.9 0.16 8 9.4 0.16 8 — — — LYD470 67126.7 — — — — — — 5.1 0.243 LYD470 67127.3 — — — — — — 5.1 0.19 3 LYD440 66903.1 75.7 0.06 9 9.50.06 9 5.3 L 7 LYD438 66898.3 — — — — — — 5.2 0.16 4 LYD438 66899.2 82.40.21 19 10.3 0.21 19 5.6 0.05 12 LYD438 66900.3 74.5 0.15 8 9.3 0.15 85.2 0.18 5 LYD414 67091.1 — — — — — — 5.1 0.25 2 LYD408 67305.6 74.40.26 8 9.3 0.26 8 — — — LYD387 67317.4 74.5 0.07 8 9.3 0.07 8 5.3 0.09 7LYD385 66893.1 — — — — — — 5.2 0.08 4 LYD385 66893.2 — — — — — — 5.20.09 5 LYD342 67063.2 — — — — — — 5.2 0.05 4 LYD337 66995.4 — — — — — —5.1 0.19 3 LYD332 66988.2 74.4 0.20 7 9.3 0.20 7 5.4 0.06 7 LYD33067046.2 83.5 L 21 10.4 L 21 5.5 0.01 11 LYD330 67050.2 — — — — — — 5.50.02 10 LYD329 67277.4 74.2 0.07 7 9.3 0.07 7 5.1 0.19 3 LYD320 67040.2— — — — — — 5.4 0.26 7 LYD318 66983.4 76.1 0.08 10 9.5 0.08 10 5.3 0.037 LYD315 67005.2 — — — — — — 5.2 0.25 3 LYD315 67007.1 75.7 0.09 9 9.50.09 9 5.3 L 7 LYD307 66975.3 — — — — — — 5.1 0.20 3 LYD307 66976.3 — —— — — — 5.2 0.09 4 CONT. — 69.2 — — 8.6 — — 5.0 — — LYD471 68050.2 48.20.06 21 6.0 0.06 21 4.3 0.09 6 LYD471 68050.4 47.6 0.02 19 6.0 0.02 194.5 0.07 10 LYD446 68109.4 45.8 0.06 15 5.7 0.06 15 4.4 L 9 LYD44668110.3 48.1 L 20 6.0 L 20 4.3 0.10 5 LYD438 66899.2 42.4 0.20 6 5.30.20 6 — — — LYD432 67961.5 — — — — — — 4.2 0.22 2 LYD422 68103.3 46.30.18 16 5.8 0.18 16 4.2 0.25 4 LYD417 68043.3 44.3 0.04 11 5.5 0.04 11 —— — LYD385 66891.2 47.1 L 18 5.9 L 18 4.3 0.02 7 LYD385 66891.3 51.90.04 30 6.5 0.04 30 4.5 0.04 10 LYD368 67660.4 45.4 0.07 14 5.7 0.07 144.2 0.11 5 LYD364 68018.3 42.2 0.21 6 5.3 0.21 6 — — — LYD364 68020.549.9 0.05 25 6.2 0.05 25 4.4 0.10 9 LYD351 68126.2 48.4 0.12 21 6.1 0.1221 4.3 0.07 6 LYD351 68129.3 45.3 0.24 13 5.7 0.24 13 4.2 0.23 3 LYD33067047.8 43.2 0.13 8 5.4 0.13 8 4.2 0.10 4 LYD315 67004.4 43.3 0.10 8 5.40.10 8 — — — LYD315 67006.2 42.2 0.24 6 5.3 0.24 6 — — — LYD315 67007.443.6 0.09 9 5.4 0.09 9 — — — LYD299 68115.4 46.1 0.07 16 5.8 0.07 16 4.30.16 6 LYD299 68118.5 45.0 0.02 13 5.6 0.02 13 4.2 0.08 4 CONT. — 39.9 —— 5.0 — — 4.1 — — LYD517 67221.3 51.3 0.17 16 6.4 0.17 16 4.5 0.23 8LYD517 67221.5 54.1 0.02 22 6.8 0.02 22 4.8 L 15 LYD517 67222.1 53.10.21 20 6.6 0.21 20 4.6 0.11 10 LYD515 67151.1 61.3 L 39 7.7 L 39 5.0 L21 LYD515 67151.6 — — — — — — 4.4 0.19 6 LYD515 67152.4 — — — — — — 4.50.17 8 LYD512 67209.1 49.2 0.14 11 6.2 0.14 11 4.5 0.10 8 LYD512 67212.256.4 0.05 27 7.0 0.05 27 4.8 0.15 15 LYD502 67342.6 53.2 0.05 20 6.70.05 20 4.6 0.04 11 LYD498 67254.3 49.2 0.19 11 6.2 0.19 11 — — — LYD48267334.1 55.2 0.15 25 6.9 0.15 25 4.7 0.16 14 LYD475 67204.2 48.0 0.28 86.0 0.28 8 4.5 0.14 9 LYD454 67193.4 54.9 0.13 24 6.9 0.13 24 4.6 0.0511 LYD452 67106.1 47.7 0.29 8 6.0 0.29 8 4.4 0.14 7 LYD452 67106.2 52.50.05 19 6.6 0.05 19 4.6 0.03 11 LYD452 67106.4 — — — — — — 4.4 0.15 7LYD452 67108.1 48.2 0.30 9 6.0 0.30 9 4.3 0.28 5 LYD451 67187.7 51.30.20 16 6.4 0.20 16 4.7 0.22 12 LYD451 67188.4 52.6 0.02 19 6.6 0.02 194.6 0.04 11 LYD450 67182.2 51.4 0.11 16 6.4 0.11 16 4.5 0.11 9 LYD44567352.3 — — — — — — 4.5 0.23 8 LYD439 6709.14 50.3 0.19 14 6.3 0.19 144.5 0.08 10 LYD439 67096.1 61.0 0.16 38 7.6 0.16 38 4.9 0.11 19 LYD41567262.1 58.2 L 31 7.3 L 31 4.9 L 18 LYD415 67264.5 49.1 0.22 11 6.1 0.2211 4.4 0.20 6 LYD415 67266.3 55.6 L 26 7.0 L 26 4.8 0.01 15 LYD41567266.6 51.7 0.04 17 6.5 0.04 17 4.6 0.07 10 LYD399 67448.3 63.9 L 448.0 L 44 5.1 L 23 LYD339 67247.3 54.4 0.01 23 6.8 0.01 23 4.8 L 16LYD328 67242.1 53.5 0.03 21 6.7 0.03 21 4.7 0.05 12 LYD324 67168.4 49.90.15 13 6.2 0.15 13 4.4 0.11 7 LYD323 67287.1 — — — — — — 4.7 0.26 14LYD323 67288.2 57.9 0.04 31 7.2 0.04 31 4.7 0.05 14 LYD321 67280.1 58.20.09 31 7.3 0.09 31 4.8 0.17 15 LYD321 67281.6 52.6 0.27 19 6.6 0.27 19— — — LYD321 67283.1 54.3 0.11 23 6.8 0.11 23 4.7 0.10 13 LYD316 67439.149.5 0.12 12 6.2 0.12 12 4.4 0.21 5 LYD312 67256.3 49.3 0.14 11 6.2 0.1411 4.3 0.25 5 LYD312 67256.4 57.2 0.09 29 7.2 0.09 29 4.7 0.18 14 LYD31267257.3 52.2 0.05 18 6.5 0.05 18 4.6 0.02 12 LYD310 67163.1 53.5 0.06 216.7 0.06 21 4.7 0.01 14 LYD309 67418.1 — — — — — — 4.4 0.22 6 LYD30967418.3 52.8 0.04 19 6.6 0.04 19 4.5 0.06 9 LYD309 67420.1 47.7 0.29 86.0 0.29 8 4.3 0.25 5 LYD296 6735.19 61.2 L 38 7.7 L 38 5.0 L 21 LYD29667359.3 63.9 0.13 44 8.0 0.13 44 5.2 0.02 26 LYD291 67400.2 47.9 0.25 86.0 0.25 8 4.4 0.12 7 LYD291 67400.5 55.9 L 26 7.0 L 26 4.7 L 13 LYD29167401.4 53.5 0.02 21 6.7 0.02 21 4.7 L 13 LYD290 67233.3 — — — — — — 4.40.17 7 LYD290 67236.4 — — — — — — 4.4 0.29 6 CONT. — 44.3 — — 5.5 — —4.1 — — LYD501 67889.1 — — — — — — 4.9 0.07 8 LYD489 67787.3 — — — — — —4.9 0.22 7 LYD453 67487.2 70.8 0.08 18 8.8 0.08 18 5.0 0.25 10 LYD44867918.2 70.5 0.02 18 8.8 0.02 18 5.0 0.02 10 LYD409 67468.1 73.2 L 229.2 L 22 4.9 0.05 9 LYD403 67770.3 67.0 0.22 12 8.4 0.22 12 — — — LYD40267762.3 78.1 L 30 9.8 L 30 5.3 L 16 LYD368 67659.1 74.3 0.27 24 9.3 0.2724 5.0 0.19 11 LYD347 67844.2 71.5 0.23 19 8.9 0.23 19 5.0 0.19 9 LYD34767845.1 — — — — — — 4.9 0.23 7 LYD347 67847.3 — — — — — — 4.9 0.27 7LYD346 67605.4 74.1 L 24 9.3 L 24 5.1 L 13 LYD346 67606.2 — — — — — —5.0 0.02 10 CONT. — 59.9 — — 7.5 — — 4.6 — — LYD483 68054.1 — — — — — —3.8 0.25 4 LYD483 68054.4 — — — — — — 3.8 0.21 4 LYD483 68056.4 36.50.22 9 4.6 0.22 9 3.9 0.25 6 LYD483 68056.5 36.2 L 8 4.5 L 8 3.9 0.01 8LYD478 67269.2 37.7 0.08 12 4.7 0.08 12 4.0 L 9 LYD478 67270.1 39.6 0.1018 4.9 0.10 18 4.0 0.03 9 LYD423 68216.2 41.1 0.17 22 5.1 0.17 22 4.10.21 13 LYD423 68218.7 38.9 L 16 4.9 L 16 4.0 0.16 10 LYD395 67077.139.0 L 16 4.9 L 16 4.0 L 10 LYD395 67080.6 38.9 L 16 4.9 L 16 3.9 0.22 7LYD392 68030.1 38.4 L 14 4.8 L 14 4.0 L 9 LYD392 68032.2 — — — — — — 4.10.16 13 LYD392 68033.3 44.4 0.13 32 5.6 0.13 32 4.2 0.14 16 LYD39268035.1 — — — — — — 3.9 0.18 8 LYD388 68096.5 — — — — — — 3.8 0.03 3LYD388 68098.4 — — — — — — 3.9 0.20 7 LYD376 68024.2 41.1 0.23 22 5.10.23 22 4.1 0.23 12 LYD376 68026.2 36.7 0.08 9 4.6 0.08 9 4.0 L 8 LYD36768066.1 — — — — — — 3.9 0.08 7 LYD367 68066.5 36.8 0.01 10 4.6 0.01 104.0 L 9 LYD367 68068.5 36.3 0.07 8 4.5 0.07 8 — — — LYD365 68092.3 35.30.24 5 4.4 0.24 5 3.8 0.10 4 LYD365 68092.4 40.4 L 20 5.1 L 20 4.0 0.0110 LYD365 68092.5 — — — — — — 3.9 0.03 6 LYD361 68146.7 40.3 0.10 20 5.00.10 20 4.1 0.08 11 LYD360 68061.2 42.2 0.06 26 5.3 0.06 26 4.1 0.12 11LYD360 68064.1 — — — — — — 3.7 0.11 3 LYD356 68139.2 39.9 0.11 19 5.00.11 19 4.0 0.16 9 LYD356 68142.2 — — — — — — 3.8 0.07 4 LYD354 68133.640.8 0.01 21 5.1 0.01 21 4.1 L 12 LYD354 68133.9 — — — — — — 3.8 0.05 3LYD354 68134.1 — — — — — — 3.7 0.13 2 LYD349 68084.1 36.3 0.26 8 4.50.26 8 3.9 0.26 5 LYD349 68085.3 40.7 0.03 21 5.1 0.03 21 4.0 L 9 LYD33266988.1 41.2 L 22 5.1 L 22 4.2 L 14 LYD332 66988.2 — — — — — — 3.9 0.167 LYD332 66989.2 — — — — — — 3.9 0.24 8 LYD325 67013.2 — — — — — — 3.80.09 5 CONT. — 33.6 — — 4.2 — — 3.7 — — ″CONT.″—Control; ″Ave.″—Average;″% Incr.″ = % increment; ″p-val.″—p-value, L—p < 0.01. The transgeneswere under the transcriptional regulation of the new At6669 promoter(SEQ ID NO: 14467). “—“ = results are still unavailable.

TABLE 63 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter RGR Of RGR Of RGR Of LeafNumber Plot Coverage Rosette Diameter Gene Event P- P- P- Name # Ave.Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD496 67741.5 0.8 0.25 14 —— — — — — LYD479 67728.5 — — — — — — 0.4 0.27 10 LYD396 67754.1 — — —7.2 0.25 16 — — — CONT. — 0.7 — — 6.2 — — 0.4 — — LYD504 67136.2 — — —10.1 0.15 16 0.5 0.15 9 LYD484 67133.3 0.8 0.10 12 — — — — — — LYD48467135.3 — — — — — — 0.5 0.29 7 LYD478 67269.2 — — — 10.2 0.11 17 0.50.02 15 LYD466 67118.1 0.9 0.01 23 — — — 0.5 0.30 7 LYD440 66903.1 0.80.03 16 9.7 0.29 11 0.5 0.20 8 LYD438 66899.2 — — — 10.5 0.07 20 0.50.04 14 LYD387 67317.4 0.8 0.13 11 — — — 0.5 0.11 11 LYD385 66893.1 — —— — — — 0.5 0.28 7 LYD375 67071.4 — — — — — — 0.5 0.21 9 LYD342 67063.2— — — — — — 0.5 0.24 7 LYD334 67294.3 0.8 0.03 17 — — — — — — LYD33266988.2 — — — — — — 0.5 0.22 8 LYD330 67046.2 — — — 10.5 0.06 20 0.50.07 12 LYD330 67050.2 0.8 0.25 9 10.1 0.16 16 0.5 0.06 12 LYD33067050.5 0.8 0.20 9 — — — — — — LYD318 66983.4 — — — — — — 0.5 0.07 12LYD315 67004.4 0.8 0.04 15 — — — — — — LYD315 67007.1 0.8 0.07 15 — — —— — — LYD315 67007.4 0.8 0.12 13 — — — 0.5 0.24 8 LYD307 66976.3 0.80.12 11 — — — 0.5 0.20 8 LYD292 66998.3 — — — 10.0 0.18 15 — — — CONT. —0.7 — — 8.7 — — 0.4 — — LYD471 68050.2 — — — 6.2 0.14 22 — — — LYD47168050.4 — — — 6.0 0.19 19 — — — LYD446 68110.3 — — — 6.2 0.15 22 — — —LYD422 68102.3 — — — 6.1 0.17 22 — — — LYD422 68103.3 — — — 5.9 0.26 17— — — LYD417 68043.1 — — — 5.9 0.28 17 — — — LYD385 66891.3 — — — 6.60.04 32 — — — LYD364 68020.5 — — — 6.4 0.09 26 — — — LYD351 68126.2 — —— 6.1 0.19 20 — — — LYD330 67046.2 — — — 6.0 0.22 19 — — — LYD30967421.4 0.7 0.16 21 — — — — — — CONT. — 0.6 — — 5.0 — — — — — LYD51767221.5 — — — 6.9 0.16 22 0.4 0.15 19 LYD517 67222.1 — — — 6.8 0.20 21 —— — LYD515 67151.1 — — — 7.9 0.02 39 0.4 0.07 24 LYD512 67212.2 — — —7.2 0.10 27 0.4 0.21 16 LYD502 67342.6 — — — 6.8 0.20 20 — — — LYD48267334.1 — — — 7.1 0.13 25 0.4 0.14 19 LYD475 67204.2 — — — — — — 0.40.20 16 LYD475 67204.4 — — — 7.1 0.14 25 0.4 0.30 15 LYD454 67193.4 — —— 7.1 0.13 25 0.4 0.30 13 LYD452 67106.2 — — — 6.7 0.25 18 — — — LYD45167188.4 — — — 6.7 0.26 18 — — — LYD439 67096.1 — — — 7.8 0.03 38 0.40.15 19 LYD415 67262.1 — — — 7.5 0.06 31 0.4 0.11 20 LYD415 67266.3 — —— 7.1 0.11 26 0.4 0.19 17 LYD399 67448.3 — — — 8.3 L 46 0.5 0.04 28LYD339 67247.3 — — — 7.0 0.14 24 0.4 0.10 21 LYD328 67242.1 — — — 6.90.17 22 0.4 0.15 18 LYD323 67287.1 — — — 7.1 0.15 24 0.4 0.26 15 LYD32367288.2 — — — 7.4 0.06 31 0.4 0.25 15 LYD321 67280.1 — — — 7.5 0.05 330.4 0.16 18 LYD321 67281.6 — — — 6.7 0.25 19 — — — LYD321 67283.1 — — —6.9 0.17 22 — — — LYD316 67437.2 — — — 6.8 0.25 20 — — — LYD312 67256.4— — — 7.3 0.07 29 0.4 0.26 15 LYD312 67257.3 — — — 6.6 0.29 17 — — —LYD310 67163.1 — — — 6.8 0.21 20 0.4 0.26 15 LYD309 67418.3 — — — 6.70.24 19 — — — LYD296 67359.1 — — — 7.9 0.02 39 0.5 0.05 25 LYD29667359.3 — — — 8.1 0.01 44 0.5 0.03 29 LYD291 67400.5 — — — 7.1 0.11 260.4 0.23 15 LYD291 67401.4 — — — 6.9 0.19 21 0.4 0.22 16 CONT. — — — —5.7 — — 0.4 — — LYD453 67487.2 0.8 0.18 17 8.8 0.14 17 — — — LYD44867918.2 — — — 8.9 0.12 17 — — — LYD409 67468.1 — — — 9.0 0.09 19 — — —LYD403 67770.3 — — — 8.5 0.28 13 — — — LYD402 67762.1 — — — 8.8 0.27 17— — — LYD402 67762.3 — — — 9.6 0.03 27 — — — LYD368 67659.1 — — — 9.30.06 23 — — — LYD347 67844.2 — — — 8.9 0.13 18 — — — LYD346 67605.4 — —— 9.2 0.06 22 0.5 0.18 12 CONT. — 0.7 — — 7.5 — — 0.4 — — LYD478 67270.1— — — 4.9 0.24 17 — — — LYD460 67930.3 0.8 0.03 36 — — — — — — LYD46067931.2 0.6 0.28 16 — — — — — — LYD423 68216.2 — — — 5.2 0.11 24 0.40.18 14 LYD423 68218.3 0.7 0.21 20 — — — — — — LYD423 68218.7 — — — 4.90.24 17 0.3 0.23 12 LYD395 67077.1 — — — 4.9 0.23 17 0.3 0.26 11 LYD39567080.6 — — — 4.9 0.25 16 — — — LYD392 68032.2 — — — 4.9 0.25 17 0.40.17 14 LYD392 68033.3 — — — 5.5 0.05 31 0.4 0.17 15 LYD392 68035.1 — —— — — — 0.3 0.27 11 LYD376 68024.2 — — — 5.2 0.14 22 0.4 0.19 14 LYD37668025.3 0.6 0.25 17 — — — — — — LYD376 68026.2 — — — — — — 0.3 0.26 11LYD367 68066.5 — — — — — — 0.3 0.24 13 LYD365 68092.4 — — — 5.1 0.14 210.3 0.24 11 LYD361 68146.5 — — — 4.9 0.28 16 — — — LYD361 68146.7 — — —5.1 0.14 21 0.3 0.22 12 LYD360 68061.2 — — — 5.3 0.10 25 — — — LYD36068063.2 0.7 0.28 18 — — — — — — LYD356 68139.2 — — — 5.0 0.21 18 — — —LYD356 68142.2 0.7 0.20 20 — — — — — — LYD354 68133.6 — — — 5.2 0.13 220.3 0.23 12 LYD349 68085.3 — — — 5.1 0.15 21 — — — LYD332 66988.1 — — —5.2 0.12 23 0.4 0.10 17 LYD332 66989.2 — — — 4.9 0.27 16 — — — CONT. —0.6 — — 4.2 — — 0.3 — — ″CONT.″—Control; ″Ave.″—Average; ″% Incr.″ = %increment; ″p-val.″—p-value, L—p < 0.01. The transgenes were under thetranscriptional regulation of the new At6669 promoter (SEQ ID NO:14467). “—“ = results are still unavailable.

TABLE 64 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Petiole Petiole PetioleRelative Area Relative Relative TP2 Area TP3 Area TP4 Gene P- % P- % P-% Name Event # Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD67310.2 11.6 0.068 14.9 14.2 0.53 2.9 520 LYD 67310.1 11.6 0.074 14.3520 LYD 67310.3 11.5 0.076 14.0 520 LYD 67313.3 11.5 0.078 13.9 520 LYD67312.1 11.5 0.085 13.2 520 LYD 67156.2 10.8 0.42  6.9 519 LYD 67157.210.7 0.43  6.5 519 LYD 67154.3 10.7 0.44  6.3 519 “CONT.” - Control;“Ave.” - Average; “% Incr.” = % increment; “p-val.” - p value, L- p<0.01. The transgenes were under the transcriptional regulation of thenew At6669 promoter (SEQ ID NO: 14467). “TP” = a relative time pointbetween measurements. “—” = results are still unavailable.

Example 18 Evaluating Transgenic Arabidopsis Under Normal ConditionsUsing In Vitro Assays [Tissue Culture T2 and T1 Plants, TC-72 and TC-T1Assays]

Surface sterilized seeds were sown in basal media [50% Murashige-Skoogmedium (MS) supplemented with 0.8% plant agar as solidifying agent] inthe presence of Kanamycin (used as a selecting agent). After sowing,plates were transferred for 2-3 days for stratification at 4° C. andthen grown at 25° C. under 12-hour light 12-hour dark daily cycles for 7to 10 days. At this time point, seedlings randomly chosen were carefullytransferred to plates containing % MS media (15 mM N). For experimentsperformed in T2 lines, each plate contained 5 seedlings of the sametransgenic event, and 3-4 different plates (replicates) for each event.For each polynucleotide of the invention at least four-five independenttransformation events were analyzed from each construct. For experimentsperformed in T₁ lines, each plate contained 5 seedlings of 5 independenttransgenic events and 3-4 different plates (replicates) were planted. Intotal, for T₁ lines, 20 independent events were evaluated. Plantsexpressing the polynucleotides of the invention were compared to theaverage measurement of the control plants (empty vector or GUS reportergene under the same promoter) used in the same experiment.

Digital imaging—A laboratory image acquisition system, which consists ofa digital reflex camera (Canon EOS 300D) attached with a 55 mm focallength lens (Canon EF-S series), mounted on a reproduction device(Kaiser RS), which includes 4 light units (4×150 Watts light bulb) andlocated in a darkroom, was used for capturing images of plantlets sawnin agar plates.

The image capturing process was repeated every 3-4 days starting at day1 till day 10 (see for example the images in FIGS. 3A-3F). An imageanalysis system was used, which consists of a personal desktop computer(Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.39[Java based image processing program which was developed at the U.S.National Institutes of Health and freely available on the internet atHypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Images werecaptured in resolution of 10 Mega Pixels (3888×2592 pixels) and storedin a low compression JPEG (Joint Photographic Experts Group standard)format. Next, analyzed data was saved to text files and processed usingthe JMP statistical analysis software (SAS institute).

Seedling analysis—Using the digital analysis seedling data wascalculated, including leaf area, root coverage and root length.

The relative growth rate for the various seedling parameters wascalculated according to the following formulas XIV (RGR leaf area), andXV (RGR root length).

Relative growth rate of leaf area=Regression coefficient of leaf areaalong time course.  Formula XIV

Relative growth rate of root length=Regression coefficient of rootlength along time course.  Formula XV

At the end of the experiment, plantlets were removed from the media andweighed for the determination of plant fresh weight. Plantlets were thendried for 24 hours at 60° C., and weighed again to measure plant dryweight for later statistical analysis. The fresh and dry weights areprovided for each Arabidopsis plant. Growth rate was determined bycomparing the leaf area coverage, root coverage and root length, betweeneach couple of sequential photographs, and results were used to resolvethe effect of the gene introduced on plant vigor under optimalconditions. Similarly, the effect of the gene introduced on biomassaccumulation, under optimal conditions, was determined by comparing theplants' fresh and dry weight to that of control plants (containing anempty vector or the GUS reporter gene under the same promoter). Fromevery construct created, 3-5 independent transformation events wereexamined in replicates.

Statistical analyses—To identify genes conferring significantly improvedplant vigor or enlarged root architecture, the results obtained from thetransgenic plants were compared to those obtained from control plants.To identify outperforming genes and constructs, results from theindependent transformation events tested were analyzed separately. Toevaluate the effect of a gene event over a control the data was analyzedby Student's t-test and the p value was calculated. Results wereconsidered significant if p≤0.1. The JMP statistics software package wasused (Version 5.2.1, SAS Institute Inc., Cary, N.C., USA).

Experimental Results:

Tables 65-67 summarize the observed phenotypes of transgenic plantsexpressing the gene constructs using the TC-T2 Assays.

The genes presented in Table 65 showed a significant improvement as theyproduced larger plant biomass (plant fresh and dry weight) in T2generation when grown under normal growth conditions, compared tocontrol plants. The genes were cloned under the regulation of aconstitutive promoter (At6669, SEQ ID NO:14467).

The evaluation of each gene was carried out by testing the performanceof different number of events. Some of the genes were evaluated in morethan one tissue culture assay. The results obtained in these secondexperiments were significantly positive as well.

TABLE 65 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Gene Dry Weight [mg]Fresh Weight [mg] Name Event # Ave. P-Val. % Incr. Ave. P-Val. % Incr.LYD480 68333.4 11.6 0.02 88 223.1 0.03 95 LYD477 68234.4 10.0 0.16 62194.1 0.12 70 LYD477 68237.2 8.6 0.14 39 170.6 0.06 49 LYD470 67126.710.0 0.06 62 181.5 0.04 59 LYD420 68342.1 14.1 0.02 128 242.3 0.02 112LYD419 67911.3 11.7 0.11 90 216.0 0.11 89 LYD418 68336.1 8.1 0.25 32 — —— LYD398 68038.2 8.0 0.29 29 152.2 0.21 33 LYD377 67952.3 8.1 0.29 31 —— — LYD358 68274.1 — — — 158.3 0.22 39 LYD352 68328.3 8.8 0.25 43 160.30.18 40 CONT. — 6.2 — — 114.3 — — LYD507 67552.3 14.5 L 133 276.8 L 125LYD507 67552.5 9.8 0.10 57 180.2 0.16 47 LYD507 67553.4 10.3 0.28 65209.9 0.24 71 LYD487 67498.1 — — — 156.7 0.24 27 LYD487 67498.3 9.8 0.0258 212.8 0.02 73 LYD487 67500.1 9.4 0.26 51 186.9 0.20 52 LYD473 67493.18.9 0.24 43 175.0 0.29 42 LYD473 67494.1 8.6 0.18 38 169.2 0.26 38LYD465 67569.2 9.6 0.03 55 189.4 0.01 54 LYD461 67522.6 9.3 0.23 49196.8 0.21 60 LYD449 67479.1 8.9 0.06 44 181.7 0.10 48 LYD449 67482.28.1 0.30 30 — — — LYD393 67563.1 11.4 0.09 82 214.9 0.09 75 LYD33167592.1 11.7 0.10 88 221.7 0.08 80 LYD331 67593.1 10.5 0.01 69 197.50.03 61 LYD327 67589.5 11.6 0.09 86 204.0 0.06 66 LYD313 67430.1 8.60.29 37 — — — LYD313 67432.1 11.9 0.09 91 223.8 0.10 82 LYD294 67406.113.1 0.03 110 274.1 0.04 123 LYD294 67407.4 8.8 0.14 41 167.2 0.21 36LYD289 67461.4 9.2 0.23 48 206.1 0.13 68 CONT. — 6.2 — — 122.9 — —LYD477 68234.1 14.1 0.12 55 270.7 0.07 77 LYD377 67952.4 12.3 0.05 35201.3 0.08 32 LYD359 67947.2 14.9 0.02 63 257.8 L 69 LYD343 67067.3 14.8L 62 269.9 L 77 LYD343 67068.6 — — — 210.3 0.26 38 LYD3 I 9 67833.3 10.50.24 15 — — — LYD295 67971.5 15.4 0.03 69 253.8 0.03 66 CONT. — 9.1 — —152.8 — — LYD507 67552.2 14.1 L 140 268.5 L 144 LYD507 67552.3 11.8 0.02101 204.2 0.06 85 LYD507 67553.5 10.3 L 76 188.6 L 71 LYD487 67496.1 7.30.26 25 — — — LYD473 67493.1 11.2 0.03 91 195.3 0.02 77 LYD393 67562.37.6 0.28 29 — — — LYD393 67563.5 10.0 0.17 71 183.9 0.22 67 LYD39067684.3 7.9 0.19 35 142.8 0.18 30 LYD390 67686.2 9.7 0.11 64 176.7 0.0560 LYD370 67665.2 8.0 0.25 36 — — — LYD370 67666.2 13.1 0.06 122 244.00.05 121 LYD340 67600.3 8.3 0.20 41 141.1 0.24 28 LYD340 67600.5 10.20.05 74 169.2 0.11 54 LYD340 67601.3 13.4 L 128 255.6 L 132 LYD33167593.5 8.3 0.16 42 158.7 0.09 44 LYD331 67594.1 9.4 0.26 60 — — —LYD331 67594.3 7.5 0.24 28 142.8 0.16 30 LYD327 67588.1 — — — 167.5 0.2452 LYD327 67589.5 10.3 0.11 75 189.2 0.07 72 LYD327 67589.6 10.3 0.03 75204.8 0.08 86 LYD313 67432.1 9.2 0.08 56 161.1 0.15 46 LYD294 67407.68.2 0.17 40 144.1 0.29 31 CONT. — 5.9 — — 110.2 — — LYD518 67750.1 15.40.05 57 241.9 0.22 27 LYD516 67743.4 16.0 0.19 63 277.8 0.24 45 LYD51667744.2 12.8 0.12 30 250.6 0.10 31 LYD516 67745.4 11.7 0.24 19 — — —LYD514 67511.4 15.9 0.02 61 278.0 0.03 46 LYD510 67828.2 19.2 L 95 341.3L 79 LYD510 67829.1 18.4 L 87 304.9 0.04 60 LYD505 67502.1 15.2 L 54268.8 0.04 41 LYD505 67505.2 14.6 0.17 48 262.1 0.22 37 LYD505 67507.214.1 0.05 43 245.7 0.26 29 LYD469 67937.2 12.1 0.19 23 — — — LYD46267868.3 19.1 L 93 337.3 L 77 LYD462 67870.1 17.3 L 76 298.7 0.01 56LYD462 67871.3 16.1 0.14 64 276.5 0.17 45 LYD462 67872.2 16.5 L 68 307.10.02 61 LYD455 67816.3 13.1 0.12 33 — — — LYD455 67817.1 12.4 0.29 26 —— — LYD424 67797.2 15.6 0.12 58 270.6 0.18 42 LYD424 67798.5 13.1 0.2433 — — — LYD419 67913.2 12.6 0.08 28 231.2 0.25 21 LYD326 67842.3 14.50.15 47 289.7 0.25 52 LYD304 67806.2 15.5 0.06 57 274.3 0.13 44 CONT. —9.8 — — 191.1 — — LYD518 67750.1 7.6 0.03 45 149.3 0.06 35 LYD51667743.4 10.6 L 101 224.0 L 103 LYD514 67508.2 8.1 0.09 54 162.0 0.06 47LYD514 67511.2 10.2 0.03 95 208.6 L 89 LYD514 67511.4 7.8 0.20 48 163.80.10 49 LYD510 67829.5 9.0 0.02 71 181.5 L 65 LYD505 67505.3 11.2 L 112204.8 0.02 86 LYD505 67507.1 8.7 0.11 66 186.7 0.07 69 LYD469 67934.38.9 0.03 70 172.6 0.07 57 LYD469 67935.3 9.0 0.10 71 182.8 0.08 66LYD469 67936.3 6.3 0.20 21 133.8 0.08 21 LYD469 67937.2 6.6 0.28 27 — —— LYD462 67868.3 6.7 0.11 27 143.0 0.06 30 LYD462 67872.2 14.1 L 169285.9 L 159 LYD455 67818.5 8.6 0.08 63 172.6 0.13 57 LYD437 67899.1 7.20.17 38 156.8 0.04 42 LYD437 67899.4 10.0 0.07 90 205.9 0.08 87 LYD43767900.1 11.5 0.01 120 214.7 0.04 95 LYD437 67900.2 8.4 0.21 60 181.70.15 65 LYD437 67902.5 9.8 0.02 88 224.6 0.03 104 LYD424 67798.5 7.70.11 47 145.4 0.15 32 LYD424 67798.6 8.0 0.10 52 160.6 0.04 46 LYD42467799.5 10.6 L 101 218.0 L 98 LYD326 67838.1 — — — 127.4 0.18 16 LYD32667839.4 10.4 L 98 202.5 L 84 LYD326 67840.1 6.6 0.15 25 — — — LYD30467805.1 6.5 0.22 23 — — — LYD304 67806.1 11.2 0.03 112 234.1 0.01 112LYD304 67806.2 13.1 0.01 150 256.8 L 133 CONT. — 5.2 — — 110.2 — —“CONT.” - Control; “Ave.” - Average; “% Incr.” = % increment; “p-val.” -p-value, L - p <0.01. The transgenes were under the transcriptionalregulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = resultsare still unavailable.

The genes presented in Tables 66 and 67 show a significant improvementin plant performance since they produced a larger leaf biomass (leafarea) and root biomass (root length and root coverage) (Table 66) and ahigher relative growth rate of leaf area, root coverage and root length(Table 67) when grown under normal growth conditions, compared tocontrol plants. Plants producing larger root biomass have betterpossibilities to absorb larger amount of nitrogen from soil. Plantsproducing larger leaf biomass have better ability to produceassimilates. The genes were cloned under the regulation of aconstitutive promoter (At6669). The evaluation of each gene wasperformed by testing the performance of different number of events. Someof the genes were evaluated in more than one tissue culture assay. Thissecond experiment confirmed the significant increment in leaf and rootperformance. Event with p-value <0.1 was considered statisticallysignificant.

TABLE 66 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Leaf Roots Coverage RootsArea [cm²] [cm²] Length [cm] Gene P- % P- % P- % Name Event # Ave. Val.Incr. Ave. Val. Incr. Ave. Val. Incr. LYD480 68331.4 — — — — — — 6.60.18 9 LYD480 68331.6 — — — — — — 6.7 0.11 11 LYD480 68333.4 0.8 L 5811.3 0.08 67 6.8 0.23 12 LYD480 68335.1 — — — — — — 6.7 0.21 10 LYD47768234.1 — — — — — — 6.9 0.06 13 LYD477 68234.4 0.8 0.07 56 9.8 0.20 456.8 0.23 12 LYD477 68237.1 0.7 0.05 31 9.3 0.11 39 7.1 0.02 17 LYD47768237.2 0.7 0.02 37 — — — — — — LYD470 67126.7 0.7 0.01 46 — — — — — —LYD420 68342.1 0.9 0.01 72 13.3 0.02 98 6.8 0.20 13 LYD420 68343.2 0.60.10 26 — — — — — — LYD420 68344.2 — — — — — — 6.6 0.24 9 LYD419 67911.30.7 0.13 45 11.2 0.20 66 — — — LYD418 68336.1 0.6 0.10 25 9.5 0.09 417.1 0.05 17 LYD398 68037.1 — — — — — — 6.7 0.10 11 LYD398 68038.2 0.60.11 24 9.5 0.10 40 6.8 0.14 11 LYD398 68038.6 — — — — — — 6.7 0.15 10LYD377 67952.3 0.7 0.06 35 9.0 0.17 34 — — — LYD377 67952.4 0.7 0.09 30— — — 7.0 0.02 16 LYD377 67953.3 — — — — — — 6.9 0.10 13 LYD358 68274.10.6 0.30 21 9.0 0.24 33 6.6 0.27 9 LYD352 68327.3 — — — — — — 6.8 0.0812 LYD352 68328.3 0.7 0.08 29 — — — — — — LYD319 67833.3 0.6 0.16 21 — —— — — — LYD509 6.1 0.89 2 CONT. — 0.5 — — 6.7 — — 6.1 — — LYD507 67552.31.1 L 85 13.3 L 44 7.9 0.16 5 LYD507 67552.5 0.8 0.09 33 — — — — — —LYD507 67553.4 0.8 0.15 37 — — — 7.9 0.26 5 LYD487 67498.3 0.8 0.02 3411.1 0.14 20 — — — LYD487 67500.1 0.8 0.13 31 11.4 0.13 24 8.0 0.06 6LYD473 67494.1 0.8 0.07 27 — — — — — — LYD465 67569.2 0.8 0.04 27 — — —— — — LYD461 67522.6 0.8 0.18 27 — — — — — — LYD449 67479.1 0.8 0.14 24— — — — — — LYD393 67563.1 0.8 0.07 37 12.7 0.10 38 8.1 0.19 8 LYD37067666.2 0.7 0.28 20 — — — — — — LYD331 67592.1 0.8 0.10 34 — — — — — —LYD331 67593.1 0.8 0.10 27 — — — — — — LYD327 67589.5 0.8 0.07 36 11.30.29 22 — — — LYD313 67430.1 0.8 0.20 22 — — — — — — LYD313 67432.1 0.90.10 47 14.3 0.12 55 8.4 0.09 12 LYD294 67406.1 0.9 0.03 48 11.9 0.18 29— — — LYD294 67407.4 0.8 0.05 28 — — — — — — LYD289 67461.4 0.9 0.06 3812.0 0.09 31 7.9 0.21 4 CONT. — 0.6 — — 9.2 — — 7.5 — — LYD477 68234.11.0 0.07 34 15.3 0.08 37 8.1 0.06 6 LYD456 67966.3 — — — 13.3 0.20 20 —— — LYD436 68073.1 — — — — — — 8.0 0.19 5 LYD377 67952.4 1.0 0.01 31 — —— — — — LYD359 67947.2 1.0 L 39 13.9 0.06 25 — — — LYD359 67947.4 0.90.18 23 — — — — — — LYD343 67064.3 0.8 0.19 14 — — — — — — LYD34367066.2 — — — 15.4 0.08 38 8.6 L 13 LYD343 67067.3 1.1 L 44 17.4 L 578.2 0.09 8 LYD319 67833.3 0.9 L 29 — — — — — — LYD295 67971.5 1.1 L 5215.6 0.06 40 8.2 0.03 8 CONT. — 0.7 — — 11.1 — — 7.6 — — LYD507 67552.21.1 L 95 14.4 0.02 67 7.8 0.09 10 LYD507 67552.3 0.9 0.01 55 13.0 L 507.9 0.03 11 LYD507 67553.5 0.8 0.01 45 11.6 0.02 35 — — — LYD473 67493.10.8 0.02 42 12.6 0.06 46 7.7 0.12 8 LYD473 67494.1 — — — 10.5 0.15 21 —— — LYD465 67569.2 — — — 10.7 0.18 24 7.9 0.11 10 LYD461 67520.5 — — — —— — 7.5 0.24 5 LYD461 67522.1 — — — — — — 7.8 0.05 10 LYD461 67522.2 0.70.22 19 10.6 0.20 23 7.6 0.23 7 LYD393 67563.5 0.8 0.20 33 — — — — — —LYD390 67683.5 — — — 10.5 0.17 22 7.6 0.27 7 LYD390 67684.3 0.7 0.19 2610.8 0.23 26 — — — LYD390 67686.2 0.8 0.03 44 12.7 0.03 47 7.6 0.17 7LYD370 67665.2 — — — 10.2 0.20 19 7.6 0.28 6 LYD370 67666.2 1.0 0.03 7811.8 0.06 36 — — — LYD370 67667.1 — — — — — — 7.5 0.24 5 LYD370 67667.4— — — — — — 7.6 0.19 7 LYD340 67600.3 0.7 0.24 21 — — — — — — LYD34067600.5 0.7 0.16 29 — — — — — — LYD340 67601.3 1.0 L 66 13.3 L 55 7.80.12 10 LYD331 67593.5 0.7 0.20 19 11.4 0.03 32 7.8 0.11 9 LYD33167594.3 — — — 10.2 0.18 19 7.6 0.17 6 LYD327 67587.4 0.7 0.08 25 — — — —— — LYD327 67588.1 0.8 0.17 44 13.6 0.12 57 8.1 0.11 13 LYD327 67588.20.7 0.27 16 10.0 0.26 16 — — — LYD327 67589.5 0.8 0.02 47 10.7 0.17 25 —— — LYD327 67589.6 0.8 0.02 40 11.1 0.12 28 — — — LYD313 67432.1 0.70.18 28 11.6 0.13 35 — — — LYD294 67407.6 — — — 12.5 0.04 45 7.7 0.10 8LYD289 67461.1 — — — 10.0 0.28 16 — — — LYD289 67461.4 — — — — — — 7.80.08 9 CONT. — 0.6 — — 8.6 — — 7.1 — — LYD518 67748.2 — — — 15.1 0.02 278.4 0.01 16 LYD518 67748.4 — — — 13.9 0.21 16 8.4 L 17 LYD518 67750.10.9 0.28 17 19.1 0.02 60 8.7 L 21 LYD518 67750.6 0.9 0.25 15 13.8 0.2315 7.8 0.14 8 LYD516 67743.4 1.0 0.15 34 17.1 0.03 44 8.4 L 17 LYD51667744.2 0.9 0.06 19 14.8 0.06 24 8.6 L 19 LYD516 67745.4 0.9 0.17 1415.1 0.06 27 8.3 L 15 LYD514 67508.1 0.9 0.15 15 16.5 0.09 39 8.1 0.0812 LYD514 67508.2 — — — — — — 7.8 0.10 8 LYD514 67511.4 1.0 L 30 15.30.09 28 8.0 0.02 11 LYD510 67828.2 1.2 L 52 17.7 L 49 8.2 0.06 13 LYD51067829.1 1.1 L 47 16.2 0.02 36 7.9 0.07 10 LYD510 67830.6 — — — 13.8 0.1115 8.0 0.01 10 LYD505 67502.1 1.0 L 34 14.2 0.06 19 7.8 0.15 8 LYD50567505.2 1.0 0.14 27 15.3 L 28 8.4 L 17 LYD505 67505.3 — — — — — — 7.80.19 8 LYD505 67507.1 1.0 0.08 24 13.5 0.27 13 — — — LYD505 67507.2 1.00.05 26 14.3 0.11 20 8.0 0.12 11 LYD469 67934.3 — — — — — — 7.9 0.03 9LYD469 67935.1 — — — 15.2 0.27 28 8.3 0.06 15 LYD469 67937.1 — — — — — —7.6 0.22 5 LYD462 67868.3 1.2 L 58 19.7 L 65 8.6 L 19 LYD462 67870.1 1.1L 45 16.0 0.01 34 8.3 L 15 LYD462 67871.3 1.1 0.08 38 16.0 0.05 34 8.00.05 10 LYD462 67872.2 1.0 L 35 17.2 L 44 8.3 L 15 LYD455 67815.1 — — —— — — 7.7 0.19 6 LYD455 67816.3 0.9 0.03 21 15.5 0.02 30 8.5 L 18 LYD45567817.1 0.9 0.29 13 — — — — — — LYD455 67818.4 0.9 0.18 11 — — — — — —LYD455 67818.5 — — — 14.4 0.05 21 7.8 0.19 8 LYD437 67899.4 — — — — — —7.8 0.06 9 LYD437 67900.1 — — — — — — 7.8 0.08 8 LYD437 67900.2 0.9 0.2222 14.1 0.18 19 7.8 0.10 8 LYD437 67902.5 — — — — — — 7.8 0.22 8 LYD42467797.2 1.1 0.02 43 15.0 0.17 26 7.8 0.13 8 LYD424 67798.5 0.9 0.13 21 —— — — — — LYD424 67799.5 0.9 0.17 12 — — — — — — LYD419 67912.4 — — — —— — 8.5 L 17 LYD419 67913.2 0.9 0.21 15 — — — — — — LYD326 67838.1 — — —— — — 8.4 L 17 LYD326 67840.1 — — — 14.0 0.08 18 8.3 L 15 LYD326 67842.31.0 0.08 25 — — — — — — LYD304 67803.3 0.9 0.29 13 15.3 L 28 8.3 L 15LYD304 67806.2 1.0 L 34 14.9 0.08 25 8.0 0.07 10 CONT. — 0.8 — — 11.9 —— 7.2 — — LYD518 67748.4 — — — 9.4 0.21 34 7.5 0.11 9 LYD518 67750.1 0.60.19 13 11.2 0.02 60 7.9 0.01 16 LYD516 67743.4 0.9 L 60 13.3 L 89 8.10.02 18 LYD516 67744.1 0.7 0.29 21 9.1 0.20 29 7.7 0.07 13 LYD51467508.1 — — — 8.8 0.06 25 7.3 0.14 7 LYD514 67508.2 0.8 0.02 37 11.6 L64 7.6 0.02 11 LYD514 67511.2 0.8 L 46 10.9 0.02 55 — — — LYD514 67511.3— — — 9.3 0.06 31 7.7 L 13 LYD514 67511.4 0.7 0.02 27 10.6 L 50 7.7 0.0213 LYD510 67828.2 — — — 10.5 0.09 50 7.8 L 14 LYD510 67829.5 0.8 L 469.9 0.01 40 — — — LYD505 67505.3 0.9 L 58 12.0 L 70 8.0 L 17 LYD50567507.1 0.8 0.07 41 9.9 0.07 40 — — — LYD469 67934.3 0.8 0.06 35 10.20.04 45 7.5 0.13 9 LYD469 67935.3 0.7 0.05 27 — — — — — — LYD469 67936.30.6 0.17 15 — — — — — — LYD469 67937.1 — — — 8.9 0.27 26 — — — LYD46967937.2 0.7 0.23 18 8.7 0.22 23 — — — LYD462 67868.3 0.7 0.09 20 9.90.04 40 7.7 0.01 13 LYD462 67871.3 0.7 0.19 18 9.4 0.11 33 7.4 0.12 8LYD462 67872.2 1.0 L 76 14.5 L 106 8.2 L 20 LYD455 67816.3 — — — 9.30.06 32 7.8 0.18 14 LYD455 67818.4 — — — 8.0 0.21 14 — — — LYD45567818.5 0.8 0.06 44 10.9 0.09 54 — — — LYD437 67899.1 0.7 L 32 — — — — —— LYD437 67899.4 0.9 0.04 61 11.0 0.09 56 8.2 L 20 LYD437 67900.1 0.9 L56 11.7 0.02 66 8.0 0.06 17 LYD437 67900.2 0.7 0.09 33 10.9 0.01 54 7.50.17 9 LYD437 67902.5 0.8 L 45 11.7 0.03 66 7.3 0.24 6 LYD424 67798.50.8 0.03 36 8.9 0.21 26 — — — LYD424 67798.6 0.7 0.04 34 — — — — — —LYD424 67799.5 0.9 L 56 10.8 0.06 53 — — — LYD326 67838.1 0.6 0.15 15 —— — — — — LYD326 67839.4 0.8 L 47 12.0 L 70 7.4 0.22 8 LYD326 67840.10.6 0.19 10 8.3 0.11 18 — — — LYD326 67842.2 0.6 0.14 13 — — — — — —LYD304 67803.1 0.6 0.27 14 9.7 0.09 38 — — — LYD304 67805.1 0.7 0.11 22— — — — — — LYD304 67806.1 0.9 L 55 12.6 0.01 79 8.0 L 17 LYD304 67806.20.9 L 65 14.3 L 103 8.0 L 17 LYD304 67807.2 0.6 0.29 17 9.2 0.23 30 7.50.03 10 CONT. — 0.6 — — 7.0 — — 6.8 — — “CONT.” - Control; “Ave.” -Average “% Incr.” = % increment; “p-val.” - p-value, L - p <0.01. Thetransgenes were under the transcriptional regulation of the new At6669promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

TABLE 67 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter RGR Of Roots RGR Of RootRGR Of Leaf Area Coverage Length Gene P- % P- % P- % Name Event # Ave.Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD480 68333.4 0.1 L 60 1.40.04 71 — — — LYD477 68234.1 — — — — — — 0.7 0.15 17 LYD477 68234.4 0.10.05 56 1.2 0.18 46 — — — LYD477 68237.1 0.1 0.24 26 1.1 0.20 38 0.80.08 24 LYD477 68237.2 0.1 0.21 27 — — — — — — LYD470 67126.7 0.1 0.0448 — — — — — — LYD420 68342.1 0.1 L 82 1.6 L 102 0.7 0.24 16 LYD41967911.3 0.1 0.06 51 1.4 0.08 72 — — — LYD418 68336.1 — — — 1.2 0.16 420.7 0.23 15 LYD398 68037.1 — — — — — — 0.7 0.16 17 LYD398 68038.2 0.10.28 24 1.2 0.15 42 — — — LYD398 68038.6 — — — — — — 0.7 0.25 14 LYD37767952.3 0.1 0.15 33 1.1 0.23 36 — — — LYD377 67952.4 0.1 0.25 26 — — —0.7 0.22 14 LYD377 67953.3 — — — — — — 0.7 0.12 19 LYD358 68274.1 0.10.24 28 1.1 0.24 36 — — — LYD352 68327.3 — — — — — — 0.7 0.19 15 LYD35268328.3 0.1 0.25 26 — — — — — — CONT. — 0.1 — — 0.8 — — 0.6 — — LYD50767552.3 0.1 L 92 1.6 0.02 44 0.8 0.03 17 LYD507 67552.5 0.1 0.03 43 — —— — — — LYD507 67553.4 0.1 0.05 44 — — — — — — LYD487 67498.3 0.1 0.0243 1.4 0.24 22 0.8 0.10 12 LYD487 67500.1 0.1 0.06 37 1.4 0.18 25 0.80.08 12 LYD473 67494.1 0.1 0.08 31 — — — — — — LYD465 67569.2 0.1 0.0830 — — — — — — LYD461 67522.6 0.1 0.16 28 — — — — — — LYD449 67479.1 0.10.11 28 — — — — — — LYD449 67482.1 — — — — — — 0.8 0.11 13 LYD39367563.1 0.1 0.03 42 1.6 0.07 39 0.8 0.11 14 LYD390 67684.2 0.1 0.30 21 —— — — — — LYD370 67666.2 0.1 0.28 20 — — — — — — LYD370 67667.1 — — — —— — 0.8 0.28 8 LYD331 67592.1 0.1 0.04 41 — — — — — — LYD331 67593.1 0.10.06 35 — — — — — — LYD327 67589.5 0.1 0.05 39 1.4 0.24 24 0.8 0.13 14LYD313 67430.1 0.1 0.20 23 — — — — — — LYD313 67432.1 0.1 0.04 48 1.80.02 56 0.9 0.03 18 LYD294 67406.1 0.1 L 52 1.5 0.13 31 — — — LYD29467407.4 0.1 0.06 32 — — — — — — LYD289 67461.4 0.1 0.03 43 1.5 0.09 310.8 0.08 12 CONT. — 0.1 — — 1.1 — — 0.7 — — LYD477 68234.1 0.1 0.03 351.9 0.03 39 0.8 0.13 13 LYD456 67966.3 — — — 1.6 0.20 21 — — — LYD43668073.1 — — — — — — 0.8 0.15 12 LYD436 68075.1 — — — — — — 0.8 0.19 11LYD377 67952.4 0.1 0.11 21 — — — — — — LYD359 67947.2 0.1 L 41 1.7 0.0827 — — — LYD359 67947.4 0.1 0.21 19 1.6 0.27 21 — — — LYD343 67064.3 0.10.22 16 — — — — — — LYD343 67066.2 — — — 1.9 0.03 39 0.8 0.07 15 LYD34367067.3 0.1 L 44 2.1 L 59 0.8 0.15 14 LYD319 67833.3 0.1 0.07 22 — — — —— — LYD295 67971.5 0.1 L 52 1.9 0.02 42 0.8 0.06 17 CONT. — 0.1 — — 1.3— — 0.7 — — LYD507 67552.2 0.1 L 103 1.7 L 70 0.7 0.22 13 LYD507 67552.30.1 0.01 55 1.6 L 53 0.8 0.05 20 LYD507 67553.5 0.1 0.02 51 1.4 0.03 390.7 0.20 14 LYD473 67493.1 0.1 0.02 48 1.5 0.02 48 — — — LYD473 67494.1— — — 1.3 0.19 23 — — — LYD465 67569.2 — — — 1.3 0.17 26 0.7 0.17 15LYD461 67522.1 — — — — — — 0.7 0.25 12 LYD461 67522.2 0.1 0.28 21 1.20.21 23 — — — LYD393 67563.5 0.1 0.15 34 — — — — — — LYD390 67683.5 — —— 1.3 0.18 25 0.7 0.28 12 LYD390 67684.3 0.1 0.18 29 1.3 0.17 26 — — —LYD390 67686.2 0.1 0.02 48 1.5 0.01 49 — — — LYD370 67665.2 — — — 1.20.24 20 — — — LYD370 67666.2 0.1 L 81 1.4 0.04 39 0.7 0.28 11 LYD37067667.1 — — — — — — 0.7 0.29 11 LYD340 67600.5 0.1 0.16 30 — — — — — —LYD340 67601.3 0.1 L 73 1.6 L 59 0.8 0.08 19 LYD331 67593.5 0.1 0.29 211.4 0.06 34 — — — LYD331 67594.1 — — — 1.4 0.15 36 0.7 0.22 15 LYD33167594.3 — — — 1.2 0.26 20 — — — LYD327 67587.4 0.1 0.17 26 1.2 0.26 22 —— — LYD327 67588.1 0.1 0.08 42 1.6 0.01 59 0.8 0.08 22 LYD327 67589.50.1 0.02 50 1.3 0.15 27 0.7 0.26 12 LYD327 67589.6 0.1 0.04 42 1.3 0.1130 — — — LYD313 67432.1 0.1 0.25 25 1.4 0.07 36 — — — LYD294 67407.6 — —— 1.5 0.02 49 0.7 0.28 11 CONT. — 0.1 — — 1.0 — — 0.6 — — LYD518 67748.2— — — 1.8 0.02 27 0.8 0.01 23 LYD518 67748.4 — — — 1.6 0.20 15 0.8 0.0518 LYD518 67750.1 0.1 0.23 18 2.3 L 60 0.8 0.01 25 LYD518 67750.6 0.10.25 16 1.7 0.18 17 0.8 0.04 17 LYD516 67743.4 0.1 0.05 37 2.0 L 44 0.80.06 18 LYD516 67744.2 0.1 0.09 22 1.8 0.05 24 0.8 0.01 24 LYD51667745.4 0.1 0.22 17 1.8 0.03 28 0.8 0.01 22 LYD514 67508.1 0.1 0.13 212.0 L 41 0.8 0.21 13 LYD514 67511.4 0.1 0.02 32 1.8 0.04 26 — — — LYD51067828.2 0.1 L 59 2.1 L 50 0.8 0.03 23 LYD510 67829.1 0.1 L 52 1.9 L 360.8 0.12 14 LYD510 67830.6 — — — 1.7 0.12 18 0.8 0.02 18 LYD505 67502.10.1 L 37 1.7 0.09 19 0.7 0.17 12 LYD505 67505.2 0.1 0.08 28 1.8 0.01 290.9 L 27 LYD505 67507.1 0.1 0.08 26 — — — — — — LYD505 67507.2 0.1 0.0627 1.7 0.11 20 0.8 0.19 13 LYD469 67934.3 — — — 1.6 0.27 14 — — — LYD46967935.1 0.1 0.26 23 1.8 0.10 28 0.8 0.04 20 LYD469 67937.1 — — — — — —0.7 0.26 9 LYD462 67868.3 0.1 L 64 2.3 L 63 0.8 0.12 16 LYD462 67870.10.1 L 50 1.9 L 34 0.8 L 25 LYD462 67871.3 0.1 0.02 40 1.9 0.01 33 0.70.25 11 LYD462 67872.2 0.1 L 40 2.0 L 43 0.8 0.12 15 LYD455 67815.1 — —— — — — 0.7 0.17 11 LYD455 67816.3 0.1 0.06 25 1.9 0.01 31 0.9 L 27LYD455 67817.1 0.1 0.29 14 — — — — — — LYD455 67818.4 0.1 0.27 14 — — —— — — LYD455 67818.5 — — — 1.7 0.07 21 — — — LYD437 67899.4 — — — — — —0.7 0.23 10 LYD437 67900.1 — — — — — — 0.7 0.20 11 LYD437 67900.2 0.10.15 23 1.7 0.17 18 — — — LYD424 67797.2 0.1 L 51 1.8 0.06 28 0.8 0.0222 LYD424 67798.5 0.1 0.08 25 — — — — — — LYD424 67799.5 0.1 0.25 14 — —— 0.8 0.12 15 LYD419 67912.4 — — — — — — 0.8 L 23 LYD419 67913.2 0.10.19 18 — — — — — — LYD326 67838.1 0.1 0.19 25 — — — 0.8 0.02 20 LYD32667840.1 — — — 1.7 0.13 18 0.8 0.03 19 LYD326 67842.3 0.1 0.04 30 — — — —— — LYD304 67803.3 0.1 0.28 15 1.8 0.02 28 0.8 0.04 19 LYD304 67806.20.1 L 38 1.7 0.07 23 — — — CONT. — 0.1 — — 1.4 — — 0.7 — — LYD51867748.4 — — — 1.1 0.07 34 — — — LYD518 67750.1 0.1 0.30 14 1.4 L 61 0.80.07 14 LYD516 67743.4 0.1 L 65 1.6 L 87 0.8 0.08 15 LYD516 67744.1 0.10.10 30 1.1 0.12 30 0.8 0.02 20 LYD516 67745.4 — — — 1.0 0.26 20 — — —LYD514 67508.1 — — — 1.1 0.13 25 — — — LYD514 67508.2 0.1 0.01 39 1.4 L62 — — — LYD514 67511.2 0.1 L 52 1.3 L 52 — — — LYD514 67511.3 — — — 1.10.06 31 0.8 0.16 10 LYD514 67511.4 0.1 0.03 30 1.3 L 47 — — — LYD51067828.2 0.1 0.22 19 1.3 0.02 46 0.8 0.14 11 LYD510 67829.5 0.1 L 54 1.20.02 38 — — — LYD510 67830.2 0.1 0.24 21 1.1 0.20 28 — — — LYD50567505.3 0.1 L 70 1.5 L 70 0.8 L 21 LYD505 67507.1 0.1 L 47 1.2 0.04 37 —— — LYD469 67934.3 0.1 0.01 41 1.2 0.02 43 — — — LYD469 67935.3 0.1 0.0432 — — — — — — LYD469 67936.3 0.1 0.13 21 — — — — — — LYD469 67937.1 — —— 1.1 0.18 25 — — — LYD469 67937.2 0.1 0.23 18 1.1 0.19 23 — — — LYD46267868.3 0.1 0.10 23 1.2 0.03 38 0.7 0.21 9 LYD462 67871.3 0.1 0.18 211.1 0.06 33 — — — LYD462 67872.2 0.1 L 91 1.7 L 104 0.8 0.01 20 LYD45567816.3 — — — 1.1 0.06 32 0.8 0.28 10 LYD455 67818.5 0.1 L 53 1.3 0.0155 0.8 0.13 13 LYD437 67899.1 0.1 L 38 — — — — — — LYD437 67899.4 0.1 L72 1.3 0.02 52 0.8 0.04 16 LYD437 67900.1 0.1 L 66 1.4 L 67 0.8 0.03 19LYD437 67900.2 0.1 0.01 43 1.3 L 54 — — — LYD437 67902.5 0.1 L 55 1.4 L66 — — — LYD424 67798.5 0.1 L 47 1.1 0.13 27 — — — LYD424 67798.6 0.10.01 41 — — — — — — LYD424 67799.5 0.1 L 69 1.3 L 54 — — — LYD32667838.1 0.1 0.20 18 — — — — — — LYD326 67839.4 0.1 L 58 1.4 L 66 — — —LYD326 67840.1 0.1 0.30 13 1.0 0.21 19 0.8 0.18 10 LYD326 67842.2 0.10.18 18 — — — — — — LYD304 67803.1 0.1 0.13 22 1.2 0.03 39 — — — LYD30467805.1 0.1 0.06 28 — — — — — — LYD304 67806.1 0.1 L 61 1.5 L 77 — — —LYD304 67806.2 0.1 L 75 1.7 L 101 0.8 0.10 13 LYD304 67807.2 0.1 0.14 241.1 0.10 31 — — — CONT. — 0.1 — — 0.9 — — 0.7 — — “CONT.” - Control;“Ave.” - Average; “% Incr.” = % increment; “p-val.” - p-value, L - p<0.01. The transgenes were under the transcriptional regulation of thenew At6669 promoter (SEQ ID NO: 14467). “—” = results are stillunavailable.

Results from T1 Plants

The genes presented in Tables 68-70 showed a significant improvement inplant biomass and root development since they produced a higher biomass(dry and fresh weight, Table 68), a larger leaf and root biomass (leafarea, root length and root coverage) (Table 69), and a higher relativegrowth rate of leaf area, root coverage and root length (Table 70) whengrown under normal growth conditions, compared to control plants. Plantsproducing larger root biomass have better possibilities to absorb largeramount of nitrogen from soil. Plants producing larger leaf biomass hasbetter ability to produce assimilates). The genes were cloned under theregulation of a constitutive promoter (At6669; SEQ ID NO: 14467). Theevaluation of each gene was performed by testing the performance ofdifferent number of events. Some of the genes were evaluated in morethan one tissue culture assay. This second experiment confirmed G thesignificant increment in leaf and root performance. Event with p-value<0.1 was considered statistically significant.

Tables 68-70 summarize the observed phenotypes of transgenic plantsexpressing the gene constructs using the TC-T1 Assays.

TABLE 68 Genes showing improved plant performance at Normal growthconditions under regulation of A6669 promoter Dry Weight [mg] FreshWeight [mg] Gene Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD46711.2 0.15 20 — — — LYD427 11.0 0.17 18 176.4 0.12 24 LYD407 11.2 0.23 20192.3 0.15 36 LYD300 10.35 0.37 11 163.7 0.27 15.5 LYD353 10.1 0.53 8.6163.2 0.33 15.1 LYD378 9.95 0.57 6.9 179.4 0.69 5.3 LYD380 — — — 147.60.76 4.1 CONT. 9.3 — — 141.8 — — LYD383 11.9 0.02 35 200.5 0.06 29 CONT.8.8 — — 156.0 — — “CONT.” - Control; “Ave.” - Average; “% Incr.” = %increment; “p-val.” - p-value, L- p <0.01. The transgenes were under thetranscriptional regulation of the new At6669 promoter (SEQ ID NO:14467). “—” = results are still unavailable.

TABLE 69 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter Leaf Area Roots CoverageRoots Length [cm²] [cm²] [cm] Gene P- % P- % P- % Name Ave. Val. Incr.Ave. Val. Incr. Ave. Val. Incr. LYD467 0.8 L 17 — — — 6.7 0.09 14 LYD4070.8 0.16 11 8.9 0.29 26 7.0 0.22 19 LYD380 — — — — — — 6.4 0.45 8.9CONT. 0.7 — — 7.1 — — 5.9 — — LYD413 — — — 8.0 0.28 21 6.6 0.14 16LYD383 0.9 0.04 35 — — — — — LYD500 0.7 0.93 8 6.7 0.9 1.8 6.1 0.55 6CONT. 0.7 — — 6.6 — — 5.7 — — “CONT.” - Control; “Ave.” - Average; “%Incr.” = % increment; “p-val.” - p-value, L-p <0.01. The transgenes wereunder the transcriptional regulation of the new At6669 promoter (SEQ IDNO: 14467). “—” = results are still unavailable.

TABLE 70 Genes showing improved plant performance at Normal growthconditions under regulation of At6669 promoter RGR Of Roots RGR Of RGROf Leaf Area Coverage Root Length Gene P- % Ave. P- % Ave. Name Ave.Val. Incr. Val. Incr. Val. Incr. P- % LYD467 0.1 0.03 20 — — — 0.7 0.1018 LYD407 0.1 0.29 10 1.1 0.10 26 0.8 0.03 26 CONT. 0.1 — — 0.9 — — 0.6— — LYD413 — — — 1.0 0.22 22 0.8 0.05 18 LYD383 0.1 L 45 — — — — — —CONT. 0.1 — — 0.8 — — 0.7 — — “CONT.” - Control; “Ave.” - Average; “%Incr.” = % increment; “p-val.” - p-value, L- p <0.01. The transgeneswere under the transcriptional regulation of the new At6669 promoter(SEQ ID NO: 14467). “—” = results are still unavailable.

These results demonstrate that the polynucleotides of the invention arecapable of improving yield and additional valuable importantagricultural traits such as increase of biomass, abiotic stresstolerance, nitrogen use efficiency, yield, vigor, fiber yield and/orquality. Thus, transformed plants showing improved fresh and dry weightdemonstrate the gene capacity to improve biomass a key trait of cropsfor forage and plant productivity; transformed plants showingimprovement of seed yield demonstrate the genes capacity to improveplant productivity; transformed plants showing improvement of plotcoverage and rosette diameter demonstrate the genes capacity to improveplant drought resistance as they reduce the loss of soil water by simpleevaporation and reduce the competition with weeds; hence reduce the needto use herbicides to control weeds. Transformed plants showingimprovement of relative growth rate of various organs (leaf and root)demonstrate the gene capacity to promote plant growth and henceshortening the needed growth period and/or alternatively improving theutilization of available nutrients and water leading to increase of landproductivity; Transformed plants showing improvement of organ number asdemonstrated by the leaf number parameter exhibit a potential to improvebiomass yield important for forage crops and improve the plantproductivity; Transformed plants showing increased root length andcoverage demonstrate the gene capacity to improve drought resistance andbetter utilization of fertilizers as the roots can reach larger soilvolume; Transformed plants showing improvement of leaf petiole relativearea and leaf blade area demonstrate the genes capacity to cope withlimited light intensities results from increasing the plant populationdensities and hence improve land productivity.

Although the invention has been described in conjunction with specificembodiments thereof, it is evident that many alternatives, modificationsand variations will be apparent to those skilled in the art.Accordingly, it is intended to embrace all such alternatives,modifications and variations that fall within the spirit and broad scopeof the appended claims.

It is the intent of the Applicant(s) that all publications, patents andpatent applications referred to in this specification are to beincorporated in their entirety by reference into the specification, asif each individual publication, patent or patent application wasspecifically and individually noted when referenced that it is to beincorporated herein by reference. In addition, citation oridentification of any reference in this application shall not beconstrued as an admission that such reference is available as prior artto the present invention. To the extent that section headings are used,they should not be construed as necessarily limiting. In addition, anypriority document(s) of this application is/are hereby incorporatedherein by reference in its/their entirety.

LENGTHY TABLES The patent application contains a lengthy table section.A copy of the table is available in electronic form from the USPTO website(https://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20210371872A1).An electronic copy of the table will also be available from the USPTOupon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

What is claimed is:
 1. A method of increasing yield, biomass, growthrate, vigor, oil content, fiber yield, fiber quality, abiotic stresstolerance, and/or nitrogen use efficiency and/or reducing time toflowering and/or time to inflorescence emergence of a plant, comprisingover-expressing within the plant a polypeptide comprising an amino acidsequence at least 80% identical to SEQ ID NO: 757, 456-599, 601-637,639-756, 758-774, 8385-8643, 8645-10582, 10587-10650, 10652-10836,10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591,12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666,12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709,12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817,12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859,12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902,12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954,12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994,12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029,13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070,13073-13076, 13079-13084, 13086-14461 or 14462, thereby increasing theyield, biomass, growth rate, vigor, oil content, fiber yield, fiberquality, abiotic stress tolerance, and/or nitrogen use efficiency,and/or reducing the time to flowering and/or the time to inflorescenceemergence of the plant.
 2. The method of claim 1, wherein said aminoacid sequence comprises conservative amino acid substitutions withrespect to a polypeptide selected from the group consisting of SEQ IDNOs: 757, 456-599, 601-637, 639-756, 758-774, 8385-8643, 8645-10582,10587-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586,12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659,12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705,12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813,12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853,12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896,12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942,12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984,12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016,13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063,13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and14462.
 3. The method of claim 1, wherein said amino acid sequence is atleast 95% identical to the amino acid sequence selected from the groupconsisting of SEQ ID NOs: 757, 456-599, 601-637, 639-756, 758-774,8385-8643, 8645-10582, 10587-10650, 10652-10836, 10838-12575, 12577,12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624,12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681,12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727,12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840,12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887,12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937,12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977,12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010,13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054,13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084,13086-14461 and
 14462. 4. The method of claim 1, wherein said amino acidsequence is selected from the group consisting of SEQ ID NOs: 757,456-459, 601-637, 639-756, 758-774, 8385-10582, 10587-10836, 10838-14461and
 14462. 5. The method of claim 1, wherein said over-expressing ofsaid polypeptide is effected by transforming a cell of the plant with anexogenous polynucleotide comprising a nucleic acid sequence encodingsaid polypeptide.
 6. The method of claim 1, further comprising selectinga plant over-expressing of said polypeptide as compared to a nativeplant of the same species under the same growth conditions and having atleast one trait selected from the group consisting of: increased yield,increased biomass, increased growth rate, increased oil content,increased fiber yield, increased fiber quality, increased abiotic stresstolerance, increased nitrogen use efficiency, reduced time to floweringand reduced time to inflorescence emergence as compared to said trait ina native plant of the same species under the same growth conditions. 7.The method of claim 6, further comprising: (a) isolating regenerableportion of said plant selected according to claim 6 so as to obtainisolated regenerable portion of said selected plants; and (b)regenerating plants from said isolated regenerable portion of saidselected plants, wherein plants without the said trait are not isolatedand not regenerated.
 8. A nucleic acid construct comprising apolynucleotide comprising a nucleic acid sequence encoding a polypeptidewhich comprises an amino acid sequence at least 80% identical to theamino acid sequence set forth in SEQ ID NO: 757, 456-599, 601-637,639-756, 758-774, 8385-8643, 8645-10582, 10587-10650, 10652-10836,10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591,12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666,12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709,12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817,12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859,12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902,12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954,12956-12%2, 12%5-12967, 12969-12977, 12979-12984, 12986-12992, 12994,12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029,13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070,13073-13076, 13079-13084, 13086-14461 or 14462 and a promoter fordirecting transcription of said nucleic acid sequence in a host cell,wherein said promoter is heterologous to said polynucleotide, whereinsaid amino acid sequence is capable of increasing yield, biomass, growthrate, vigor, oil content, fiber yield, fiber quality, abiotic stresstolerance, and/or nitrogen use efficiency, and/or reducing time toflowering and/or time to inflorescence emergence when over-expressed ina plant as compared to a native plant of the same species which is grownunder the same growth conditions.
 9. The nucleic acid construct of claim8, wherein said amino acid sequence comprises conservative amino acidsubstitutions with respect to a polypeptide selected from the groupconsisting of SEQ ID NOs: 757, 456-599, 601-637, 639-756, 758-774,8385-8643, 8645-10582, 10587-10650, 10652-10836, 10838-12575, 12577,12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624,12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681,12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727,12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840,12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887,12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937,12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977,12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010,13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054,13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084,13086-14461 and
 14462. 10. The nucleic acid construct of claim 8,wherein said amino acid sequence is at least 95% identical to the aminoacid sequence selected from the group consisting of SEQ ID NOs: 757,456-599, 601-637, 639-756, 758-774, 8385-8643, 8645-10582, 10587-10650,10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590,12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666,12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709,12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817,12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859,12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902,12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954,12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994,12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029,13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070,13073-13076, 13079-13084, 13086-14461 and
 14462. 11. The nucleic acidconstruct of claim 8, wherein said amino acid sequence is selected fromthe group consisting of SEQ ID NOs: 757, 456-599, 601-637, 639-756,758-774, 8385-10582, 10587-10836, 10838-14461 and
 14462. 12. A plantcell comprising a nucleic acid construct comprising an isolatedpolynucleotide comprising a nucleic acid sequence encoding a polypeptidewhich comprises an amino acid sequence at least 80% identical to theamino acid sequence set forth in SEQ ID NO: 757, 456-599, 601-637,639-756, 758-774, 8385-8643, 8645-10582, 10587-10650, 10652-10836,10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591,12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666,12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709,12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817,12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859,12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902,12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954,12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994,12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029,13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070,13073-13076, 13079-13084, 13086-14461 or 14462 and a promoter fordirecting transcription of said nucleic acid sequence in a host cell,wherein said promoter is heterologous to said isolated polynucleotideand/or to said plant cell, wherein said amino acid sequence is capableof increasing yield, biomass, growth rate, vigor, oil content, fiberyield, fiber quality, abiotic stress tolerance, and/or nitrogen useefficiency, and/or reducing time to flowering and/or time toinflorescence emergence when over-expressed in a plant as compared to anative plant of the same species which is grown under the same growthconditions.
 13. The plant cell of claim 12, wherein said amino acidsequence comprises conservative amino acid substitutions with respect toa polypeptide selected from the group consisting of SEQ ID NOs: 757,456-599, 601-637, 639-756, 758-774, 8385-8643, 8645-10582, 10587-10650,10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590,12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666,12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709,12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817,12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859,12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902,12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954,12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994,12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029,13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070,13073-13076, 13079-13084, 13086-14461 and
 14462. 14. The plant cell ofclaim 12, wherein said amino acid sequence is at least 95% identical tothe amino acid sequence selected from the group consisting of SEQ IDNOs: 757, 456-599, 601-637, 639-756, 758-774, 8385-8643, 8645-10582,10587-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586,12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659,12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705,12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813,12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853,12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896,12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942,12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984,12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016,13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063,13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and14462.
 15. The plant cell of claim 12, wherein said amino acid sequenceis selected from the group consisting of SEQ ID NOs: 757, 456-599,601-637, 639-756, 758-774, 8385-10582, 10587-10836, 10838-14461 and14462.
 16. The method of claim 5, wherein said nucleic acid sequence isselected from the group consisting of SEQ ID NOs: 377, 1-182, 184-376,378-398, 400-436, 438-455, 775-3902, and 3909-8384.
 17. The plant cellof claim 12, wherein said plant cell forms part of a plant.
 18. Themethod of claim 1, further comprising growing the plant over-expressingsaid polypeptide under the abiotic stress.
 19. The method of claim 1,wherein said abiotic stress is selected from the group consisting ofsalinity, drought, water deprivation, flood, etiolation, lowtemperature, high temperature, heavy metal toxicity, anaerobiosis,nutrient deficiency, nutrient excess, atmospheric pollution and UVirradiation.
 20. A transgenic plant comprising the nucleic acidconstruct of claim
 8. 21. A method of generating a transgenic plant,comprising expressing the nucleic acid construct of claim 8 within theplant, thereby generating the transgenic plant.
 22. The method of claim1, further comprising growing the plant over-expressing said polypeptideunder nitrogen-limiting conditions.